The Bundesliga champions, chasing a fifth continental crown, will play Borussia Dortmund in the May 25 final at London's Wembley Stadium after an imperious performance that inflicted the heaviest two-legged European defeat in Barca's history.
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Last year's runners-up Bayern had effectively killed off the tie with last week's 4-0 victory in Munich and there was no way back for a toothless Barca when Arjen Robben cut inside and blasted the ball past Victor Valdes in the 49th minute.
"We played an outstanding game but there is a difference of Barca with and without Messi," Bayern coach Heynckes told ZDF television as the German domination of Spain was completed following Dortmund's win over Real Madrid on Tuesday.
"But it is a result one could not forecast," added the former Real Madrid and Athletic Bilbao boss.
"I know the philosophy of Barcelona and my team understood extremely well how to deploy our tactics.
"It was harder than it looked. My team was very focused... we knew what we were up against."
"We would have liked to play at the same level as Bayern but we can only congratulate them now and get back to work," Barca coach Tito Vilanova, who took over from his close friend Guardiola at the end of last season, told a news conference.
Fabregas was initially deployed in Messi's roving forward role in a three-pronged attack with Spain team-mates Pedro and Villa.
