Heynckes, who will be replaced at Leverkusen by Freiburg boss Robin Dutt, said he had yet to decide whether to return to struggling Bundesliga champions Bayern once Louis van Gaal leaves at the end of this campaign.
"I have not said yes and no negotiations have taken place with Bayern until now," he said in a statement, adding Bayern CEO Karl-Heinz Rummenigge had called him "to offer the position".
"Then I also talked with my good friend (Bayern president) Uli Hoeness."
Heynckes' most recent of two stints at Bayern was in 2009 when he took over for the last five games of the season to help them clinch second spot and Champions League qualification after the sacking of Juergen Klinsmann.
"Leverkusen is a well managed club with a great team and it was difficult taking this decision," the 65-year-old said in an earlier statement.
"I will do everything so we finish second in the league and qualify directly for the Champions League."
"Robin Dutt was always going to be our first choice to succeed Heynckes whether in 2011 or 2012," said Leverkusen sports director Rudi Voeller.
"I am looking forward to the challenge that is Leverkusen," said Dutt. "Bayer's philosophy is in line with my views on football."
Marcus Sorg, who coaches Freiburg's reserves, will take over the senior team when Dutt leaves, the club said.
