The 72-year-old German returns to take charge of the Bundesliga champions for a fourth time after Carlo Ancelotti was sacked last month following a 3-0 defeat to Paris Saint-Germain.
Former Borussia Dortmund boss Thomas Tuchel and Hoffenheim manager Julian Nagelsmann had been both thought to fill the vacant role at Allianz Arena but Bayern have instead turned to the experience of Heynckes, who won a Bundesliga, German Cup and Champions League treble during his last spell with the Bavarians.
He retired from management in 2013 but admits the offer to take charge of his former side was too good to turn down.
“I wouldn’t have returned to any other club in the world, but FC Bayern München are very close to my heart,” said Heynckes, in a statement on Bayern’s website.
“My coaching staff and I will now do everything to bring back successful football for the fans. I’m very much looking forward to this challenge.”
The Bundesliga club chief executive Karl-Heinz Rummenigge believes Heynckes is the right man to bring the club’s glory days after a disappointing start under Ancelotti.
“There’s a great mutual trust between Jupp Heynckes and FC Bayern,” he said. “That showed itself again in the conversations that [club president] Uli Hoeneß, [sporting director] Hasan Salihamidžić and I have had with him.
“We’re very thankful to Jupp that he’s accepted the offer of head coach. He’s the ideal man for FC Bayern at this moment in time.”
Bayern Munich currently trail rivals Borussia Dortmund by five points in the Bundesliga, while they also find themselves second in their Champions League group, three points behind Paris Saint-Germain.
Jupp Heynckes will take charge of his first game as Bayern’s head coach when the club host Freiburg on October 14 after the ongoing international break.