The last time the showpiece fixture was held at the stadium was 2007, when Wasps beat Leicester.
The match will take place on the weekend of 19-20 May 2012 and will be the fourth time the London ground has staged a European final.
Next season's competition will begin three weeks later than usual, on the weekend of November 11-13, to allow for the end of the New Zealand World Cup.
The international tournament reaches its climax at Eden Park in Auckland on 23 October.
The Amlin Challenge Cup will begin on the same weekend as the Heineken Cup, with a second set of fixtures taking place the following weekend.
There will then be a set of back-to-back matches in both competitions in December (8-11 and 15-18) and January (12-15 and 19-22).
Quarter-final ties will be played over the weekend of 5-8 April 2012 and the semi-finals will take place between 27-29 April.
The Challenge Cup final will be contested on the same weekend as the Twickenham final, at a venue which has yet to be confirmed.
Toulouse beat Biarritz to win the 2010 Heineken Cup in Paris, while Cardiff Blues defeated Toulon in Marseille to take last year's Challenge Cup.
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