UEFA announced the fines on Thursday after a meeting of the organisation's control and disciplinary board.
England were charged over the improper conduct of their fans, while Croatia were charged with several offences including "a serious lack of organisation" and "the selling of tickets on match day without the approval of the police, English FA or UEFA."
Further charges related to the throwing of projectiles by Croatian fans and the setting off of flares within the stadium.
Croatia beat England 2-0 in the Group E qualifier.
A police statement issued after the match said that 187 Croatian fans and 31 English supporters were detained for incidents away from the ground.
A further 25 England fans were arrested inside the stadium following a clash with stewards at one of the gates.
Both associations are entitled to appeal within 72 hours of receiving written notice of the fines.