This couldn't exist without the work done by several people in the MacRumors forums, and the following is a copy & paste from a posting by rew, found in its original here.

What we're doing in a nutshell:
We're going to buy the PC version of an ATI 4870 video card because they're going to cost a good deal less than the official cards from Apple. The firmware on these PC cards is NOT compatible with our Mac Pros, however. Our goal then is to essentially update this firmware with something that our Mac Pros can understand. This is a slightly tricky process since we can't update the firmware from within OS X, and so we'll first have to boot to a DOS environment, flash the card from there, and then install the drivers for the video card onto OS X just like we would with Windows. Folks HAVE been able to flash directly from Windows, I just wasn't able to do it myself.

The end result:

**Assumptions: **
You have a Mac Pro and you have Bootcamp installed on that Mac Pro (alternatively, if you have a PC in addition to your Mac Pro, you may execute the first two phases of the directions below on your PC and just transfer the card to your Mac when finished with phase two). You use a DVI connection between your monitor and your current video card. You have Windows XP installed on Bootcamp (Vista is probably fine, but I did NOT test it). You're somewhat of a power user and know how to make your way around DOS, are comfortable with ISO files, and have no issues with modifying system files. This isn't brain surgery, but you should be able to follow along with what's going on lest you run into problems. If this isn't you, then you shouldn't try this.

This guide is for a stock Mac Pro purchased in August of 2006. It had one 7300GT card and upgraded RAM and an additional CD-ROM drive, but past that, all stock.
I haven't seen any specific instructions for specific Mac Pro models, so if you have a newer Mac Pro these directions MAY still be sufficient. Newer Macs will likely work, but obviously I haven't been able to test them.
There are numerous methods that folks have used to flash their cards. Some used WinFlash (flash your card from within Windows), some used a version of DOS (what we will be doing), and some used a standalone PC to boot into DOS, flash the card, and drop the card into the Mac. The point being that you don't HAVE to do it this way - I have Windows and Bootcamp installed, you might not want to install those if you don't already have them. At any rate, there ARE other methods, this is just the method I chose.
Obviously proceed with care - I'm not responsible for any damage you may do to your computer and flashing cards can be serious business.

What you need to buy (HARDWARE):
This EXACT Sapphire video card: SAPPHIRE 100259-1GL Radeon HD 4870 1GB 256-bit GDDR5 PCI Express 2.0 x16 HDCP. PN# 288-20e85-130sa SKU# 11133-04-20r. You can buy it HERE.
TWO of these EXACT internal power cables. The Sapphire comes with power cables, but they won't fit in our Mac Pros, so we need to get these instead. You can buy them HERE. Alternatively, some folks have crafted their own cables. Instructions are present earlier in the thread.

What you need to download (SOFTWARE):
GPU-Z. We're going to use this Windows application to safely backup the factory ROM on the card in case something goes wrong. Get it HERE
evlisizer's ROM. This is the firmware that we will be placing on the card. Get it from HERE (it's the attachment)
ATIFlash. This is the application that will copy elvisizer's ROM onto the card. Get if from HERE
The OS X Radeon Drivers. These enable full support of the card (minus the second DVI port) within OS X. Get them (if they're not present, Google for "MacOSX_10.5.6_radeon_hd_48x0_drivers.pkg") HERE
Ultimate Boot CD: We are going to make a bootable CD that will get us into a DOS environment where we can flash the card. Download the ISO version from HERE
MagicISO: When we boot off of our Ultimate Boot CD, we're going to need to have ATIFlash and the new ROM file also burned onto the CD so that we can flash the ROM. We're going to use MagicISO to open the iso file from Ultimate Boot CD and put those files into the ISO before we burn it.

Assuming you've met the assumptions and have all of the hardware and software, here are the Step-By-Step Directions:

Stage one: Install the card, backup the ROM, setup the boot CD.
Install the new 4870 in the first slot (your primary card is probably sitting here). Move the card that resides in that slot to the second slot. Install both of the power cables (if your Mac Pro is upgright and you're looking into it, then the connectors are toward the upper left of the motherboard). Use some caution here - it's a snug fit.
Plug the DVI cable into your OLD video card, NOT the new card. This might just have been my computer, but when I tried to view any sort of video through the new card (even in Windows) it didn't put out a signal in either DVI ports. Don't be concerned if this happens to you.
Turn your Mac on. Using Bootcamp, load Windows. When Windows is loaded, you should see that it found the 4870. Don't worry about installing the drivers for it yet, we just want to make sure that you have the card and power cables installed correctly and that Windows can see it.
Open GPU-Z. At the bottom of the application, you'll see a dropdown box, probably with your old video card selected. Select the new card. Next to the "BIOS Version" label, you'll see a small icon of a chip with a green arrow. Click it and save the resulting file in a safe location - THIS IS YOUR BACKUP ROM.
Open MagicISO. Load the Ultimate Boot CD ROM. In the upper right window, create a new folder and call it "Mac". In this folder, add the contents of the file that you downloaded (don't just put the zip file in here, unzip it and dump the contents!) and the "pc4870.rom" file that is in the "" file you downloaded. I also threw "MacOSX_10.5.6_radeon_hd_48x0_drivers.pkg" in this directory just so that I had the files handy for OS X. Once you have the files in place, save the ISO.
Burn the ISO file to a CD.

Stage two: Flash the video card
With the CD we created in step 6, reboot your computer and hold down the "Alt" key to bring up the Bootcamp Bootloader. On the very right, you should see an option to boot from the CD. Do this. As it loads, you'll see another screen asking you to hit enter to boot from the CD. Do it.
At the main menu, select the "DOS/Linux Boot Disks" option.
Select the OpenDOS Boot Disk. You may have to hit "enter" a few times here. I didn't do anything fancy here, just let it run through the process and pretty much said "yes" for everything. Keep your eye open to see which letter it maps your CD to - mine was something like T:.
Navigate to your CD's "Mac" directory that we setup in step 5.
Type "ATIFlash -i" and hit enter. This will display information about the ATI cards on your system. Again, we're just ensuring that the card is being read and is ready to be flashed. Don't be concerned if you only see one card here even if you have two installed - this will ONLY show ATI cards that are installed, and so it ignored my Nvidia 7300 GT.
Time to flash the card. Assuming your situation is similar to mine and the above only shows one single card, type "ATIFlash -p 0 pc4870.rom -f" and hit enter. You should see a successful message telling you that your card has been updated and to restart. If two cards show up, I BELIEVE you will substitute the "0" for whichever number (from the above stuff) the 4870 is in.
Turn your Mac off. Pull out the old video card and plug your monitor into the new video card. Only one of the DVI outputs works - I think it's the upper one.
Power back on. With any luck your screen will light up and OS X will load! If you've gotten this far, then you're pretty much golden.

Stage three: Install the drivers for OS X (Enter your password as necessary)
OS X will now load. It may look completely fine, but the drivers aren't installed yet and so you'll be getting degraded video performance and Quartz Extreme won't be supported (you can see that in the System Profiler). Assuming you still have the boot CD in your drive, open it and navigate to the "Mac" directory. Copy the "" and "MacOSX_10.5.6_radeon_hd_48x0_drivers.pkg" files to your desktop.
Install the "MacOSX_10.5.6_radeon_hd_48x0_drivers.pkg" file.
Reboot! When you get back into OS X, if you look at your video card under System Profiler, you should see that your card now supports Quartz Extreme.

Finished! The only thing you probably still need to do is install video card drivers in Windows. Those came with your video card's CD.

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