The Bavarian side took the semi-final second leg against the Catalans 3-0, who crashed out 7-0 on aggregate, to set up a clash with Borussia Dortmund.
It is Bayern’s third Champions League final in four years, and the first all-German final.
Arjen Robben opened the scoring for the visitors, before an own goal from Gerard Pique and Thomas Muller’s strike 14 minutes from time.
In the build up to the game it was revealed that Lionel Messi would not be available from the start.
Both teams spent the first 20 minutes on the attack, but there were few chances.
The hosts were forced to try their luck from range against an organised Bayern defence, and Pedro came close from 35 metres out, but his shot was parried by Manuel Neuer.
Xavi had a rare chance in the first half, after Dani Alves sent a cross in to Cesc Fabregas in the box, but he sent his volley way over the crossbar.
Three minutes into the second half the Germans all but sealed the semi-final, when David Alaba sent a cross-field ball to an unmarked Arjen Robben. The Dutchman cut back past Adriano and hit home into the corner of goal, leaving Victor Valdes, in his 100th Champions League appearance, no chance.
With 18 minutes to go, Pique sent a cross into his own net, before Muller rose to head in the third.
The final will take place on May 25 in Wembley.