The Bantams eventually fought their way past the Cobblers after a replay, extra-time and penalties before drawing their 2nd Round tie with Brentford on Friday night.
Ahead of the planned replay, however, the FA have ruled that Bradford breached the rules by fielding Newcastle United loanee Curtis Good in the original game.
An FA statement read: 'The FA has confirmed that Bradford City have been removed from The FA Cup with Budweiser 2012-13 competition after fielding an ineligible player in their second-round tie against Brentford.'