Depending on the revision of your board, the BIOS updates for it are available here: GIGABYTE - Support & Downloads - Downloads
First, make sure the update you're using matches the revision of your board - otherwise, it won't work.
Next, I downloaded the files and all appear to indeed be DOS-only utilities (running from autoexec.bat, no less). You will need a bootable DOS floppy disk to run this - you can get disk images from bootdisk.com
(download one of the three links to the right of "Driver Free Disk For BIOS Flashing") that, when run, will place the image on a 1.44MB floppy disk. Once you've created the floppy from the downloaded image file, you can then copy the contents of the BIOS utility (including the .exe file, the .F11 file, autoexec.bat, and any other files included in the download) onto that floppy. Once you do that, you can boot to that floppy disk and it will start the flash process for the BIOS automatically.
However and again, this is NOT something you can run from Windows (or even WinPE) - it *MUST* be run from *REAL DOS*. I cannot imagine why in today's day and age (well, this was released in 2009, anyway) we still have BIOS and motherboard makers shipping systems that must be flashed from a utility run from DOS. Bootable (and free to use) Windows PE environments have been around since 2006, and PE itself has been available to system makers since at least 2002.