But following the sacking of Carlo Ancelotti on 28 September, Bayern have been without a head coach.
Assistant coach Willy Sagnol took charge of Bayern's Bundesliga game on 1 October at Hertha Berlin. But the former Bayern defender's moment in the hot seat was marred by a disjointed performance in which his players squandered a two goal lead to draw 2-2 and fall five points behind leaders Borussia Dortmund after seven games.
Heynckes first led Bayern from 1987 to 1991, then briefly in 2009 as caretaker, and from 2011 until 2013. Pep Guardiola took over from the former Germany international.
"There is a strong relationship of trust between Jupp Heynckes and FC Bayern," said club chairman Karl-Heinz Rummenigge. "He is at the moment the ideal coach for Bayern."
Heynckes will be assisted by the co-trainer of Fortuna Duesseldorf, Peter Hermann, and the sports director of Bayern's youth team, Hermann Gerland. The troika led Bayern to their famous treble.
"I would not have returned to any other club in the world, but Bayern Munich is close to my heart," said Heynckes, vowing to transform the team back into a successful squad.
In an interview with Kicker magazine, Heynckes said he was not making a comeback adding: "It's a service for a friend. I'm doing it only because I owe a lot to Bayern."