Heynckes had tasted victory in the Champions League before, in 1998 when he managed Real Madrid.
"The game was very difficult because of the opponent's league predicament, " coach Jupp Heynckes told reporters.
First, Heynckes pointed to the Croatian national team striker Mario Mandzukic, who scored Bayern's third goal.
Heynckes's win percentage stands at 71%, compared with Guardiola's 74%, according to Opta Sports.
Jupp Heynckes' men will be the heavy favorite in the German Cup final on June 1 against VfB Stuttgart.
"The fact that we have won the title after 28 games is extraordinary, it's simply fantastic, " Heynckes told reporters.
Heynckes was Real's coach in 1998, when Madrid won their first title in the competition in more than 30 years.
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Heynckes is currently in his third spell as Bayern coach having taken over from Dutchman Louis van Gaal in 2011.
Heynckes is an intense, red-faced taskmaster, whose side is so organized that the players practically move in lock-step with each other.
Aside from one-syllable takes on the name Joseph, Guardiola and Heynckes don't have much in common, at least on the surface.
The news of Guardiola's appointment coincided with the announcement that 67-year-old current Bayern coach Jupp Heynckes will be retiring from coaching.
Bayern manager Jupp Heynckes said that during the club's last training session, he'd told Robben he could make the difference on Saturday.
But undefeated Leverkusen made no mistake with the Bundesliga top scorer Kiessling leading the way for Jupp Heynckes' men after 22 minutes.
That version of events has been pushed recently by reports out of Germany that Schalke was looking to hire Heynckes for next season.
Heynckes compounded the rumors around him by dropping a strong hint after the game that he would be a Bayern player by this fall.
And Villas-Boas says he was shocked when Bayern announced Guardiola would take over from current coach, Jupp Heynckes, at the end of this season.
It's just as telling that Heynckes was able to leave two world-class internationals on the bench in Germany's Mario Gomez and the Netherlands' Arjen Robben.
From July, he will replace Jupp Heynckes, who led Bayern Munich to a Champions League final and a second-place finish in the league last season.
The biggest argument in favor of changing direction is Heynckes's age.
Even Heynckes admitted in January that "a club like Bayern has to think and act with an eye to the future, " according to the club's website.
"I wouldn't say that we witnessed the end of an era, " said Heynckes, who will be replaced at Bayern by former Barcelona manager Pep Guardiola next season.
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"You've got to take into consideration that Arsenal are actually competing with teams like Chelsea, Manchester United and Manchester City, " Heynckes said in German through an interpreter.
With that and his already secured Bundesliga title, Heynckes would complete a stunning treble before he leaves the club to be replaced by former Barcelona manager Pep Guardiola.
Still, Bayern manager Jupp Heynckes didn't buy into the narrative of a power shift in European soccer or indeed that Barcelona's remarkable run of success was suddenly hitting a wall.
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It's not merely a question of age: The men who won the league titles in Germany and England this year, Jupp Heynckes and Alex Ferguson, are 68 and 71 respectively.
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"FC Bayern today announces that head coach Jupp Heynckes has decided to retire when his current contract expires on 30 June 2013, " read a statement on the German league leader's website.
Bayern's manager Jupp Heynckes, at least, sympathizes with Wenger.
Any managerial change brings with it an increased chance of player moves and no doubt Guardiola will bring in a couple of players when he finally takes over from Jupp Heynckes this summer.
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