The "monkey chants" occured firstly in the Under 21's game, and targeted especially at Darren Bent and Carlton Cole upfront. Then it carried on the following evening in the seniors game when the "monkey chants" worsened.
England's black players were verbally abused by fans at both the Under-21 game, and the senior side's match at El Santiago Bernabeu.
Fifa announced the punishment following a meeting of their disciplinary committee in Zurich on Tuesday.
In a statement, world football's governing body warned that any repeat of such racist abuse could lead to Spain having to play future matches behind closed doors or even expulsion from major tournaments.
The news is bound to dismay some in the game who had called for that kind of harsh punishment this time around to try and help eradicate the problem.
Spain manager Luis Aragones is currently under investigation by the RFEF for comments made about Arsenal's Thierry Henry and England's colonial past prior to the game on November 17.
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