The Bantams did not receive written permission for Curtis Good, on loan from Newcastle, to play in the competition by the 12pm deadline on the day of the fixture, which ended 1-1 at Valley Parade.
The club said they have appealed, a process that will take place throughout the forthcoming week.
If unsuccessful, Brentford would progress to the third round to play Bury or Southend.
The FA said on the FA Cup website: "Bradford City have been removed from The FA Cup 2012-13 competition after fielding an ineligible player in their Second Round tie against Brentford."
The replay was scheduled to take place at Griffin Park on Tuesday December 18.