The club was thrown out of the competition on 7 December after defender Curtis Good, on loan from Newcastle, played for the Bantams in their 1-1 draw at Valley Parade on 30 November.
Good was not registered with the FA in time for their 12pm deadline ahead of the Friday night game though, leading to their expulsion from the competition.
But the West Yorkshire side successfully appealed the decision and will now travel to Griffin Park for the FA Cup replay next Tuesday, with the winners then facing Southend in the third round.
Bradford will now pay a £1,000 fine instead.
Bury and Droylsden lodged appeals with the FA in 2006 and 2008 respectively after they too fielded ineligible players, although both clubs argued their cases unsuccessfully.
The news comes a day after Bradford secured their place in the semi-finals of the Capital One Cup after they beat Arsenal in a penalty shootout.
Phil Parkinson's side are also in the latter stages of the Johnstone's Paint Trophy.
A Bradford statement read: "Bradford City FC can confirm that today director of operations David Baldwin attended an appeal hearing with Ben Jones, Partner at Petherbridge Bassra solicitors and Mr Simon Csoka QC of Carmelite Chambers.
"The appeal was heard before the FA Appeal committee at Wembley Stadium in relation to the matter of the club's expulsion from this season's FA Cup with Budweiser competition.
"We can confirm that on appeal the club has now been reinstated back into the FA Cup competition and has been fined for its actions.
"We deeply regret our breach of the rules and are currently reviewing our procedures to ensure no repeat of this situation.
"Therefore the original replay of the club's FA Cup second-round tie at Brentford FC, scheduled for Tuesday, December 18 2012, will now take place at the Bees' Griffin Park stadium."