Both clubs have also been warned about their future conduct after the incident in the FA cup replay.
Bradford City have been fined £3,000 after admitting a breach of FA Rules in relation to their FA Cup Third Round replay with Championship side Millwall at the Coral Windows Stadium on Wednesday 14 January 2015.
Millwall have been fined £6,000 for their part in a melee that was sparked when Lions defender Alan Dunne barged City striker James Hanson off the pitch and into an advertising board.
The charge was that in or around the 28th minute of the fixture, both clubs failed to ensure their players and/or officials conducted themselves in an orderly fashion and/or refrained from provocative behaviour.
As well as being fined, both City and Millwall have also warned as to their future conduct.