Hoeness has now confirmed that Bayern wanted Heynckes to remain in charge, while Thomas Tuchel - sacked by rivals Borussia Dortmund less than a year ago - was also contacted but rejected the offer.
"It was portrayed as having a desperate search. We tried for a very, very long time to persuade Jupp [to stay on]. When we realised in a final, final conversation that he was not doing it, we were talking to the coach who was free, Thomas Tuchel," Hoeness told reporters.
"He told us that he had already decided. That was a shame, but not a shock for us. He also had no contract offer, but it was the offer of a mutual conversation with us both, with Hasan he had met before. Then a few days later we met again internally and decided that our preferred candidate is now Niko Kovac. And that's how it happened."
Tuchel is rumoured to have agreed a deal to take over as Paris Saint-Germain's next manager, while Arsenal and Chelsea have also been linked.