He becomes the fourth Dutch coach at Barca following Johan Cruyff, Louis van Gaal and Rinus Michels.
Heynckes is currently in his third spell as Bayern coach having taken over from Dutchman Louis van Gaal in 2011.
Just three lasted more than 12 months: Louis Van Gaal at Bayern Munich, Reynald Denoueix at Real Sociedad and Bert Van Marwijk at Borussia Dortmund.
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Three weeks ago, Nigeria named a list of preferred candidates, and since then Louis Van Gaal, Guus Hiddink and Peter Taylor have all rejected the chance to coach Nigeria.
Later on Sunday, Bayern Munich eased a little of the pressure on coach Louis van Gaal with a 3-0 win over Hannover to move to fourth in the Bundesliga.
Bayern coach Louis van Gaal replaced Gomez with Franck Ribery in the second half, and the Frenchman was involved as Bastian Schweinsteiger made it 2-1 with a low shot from outside the area.
Louis van Gaal had said before the game that his job as Bayern coach was on the line and his side's fourth draw at the Allianz Arena this season hardly improves the Dutchman's position.
The 32-year-old Italian international has struggled to hold down a place at Bayern under new coach Louis van Gaal and is keen to secure regular football in a bid to force his way in Italy coach Marcello Lippi's World Cup plans.
He worked with Guus Hiddink, Frank Rijkaard, Louis van Gaal and Dick Advocaat at three World Cups and three European Championships with Netherlands, Russia and Korea, as well as with the Korean national team at the 2010 World Cup finals in South Africa.
However, Inter will argue they deserved their slice of luck, and the match-up of Mourinho against Bayern boss Louis van Gaal, one of the men under whom he served his apprenticeship at Barca, provides a fascinating back-drop to what will be an hotly-contested final next month.
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