Kovac took over Eintracht Frankfurt in March 2016 and helped the club survive a relegation playoff that season before finishing 11th past year.
He rescued the Eagles from the brink of relegation in his first season, led them to the German Cup final in his second, and has guided them to the brink of Champions League football this year - one of the league's indisputable success stories.
Kovac said last week he was happy at Eintracht, where his contract runs for another season, but he left the door open for a possible change.
"I hope Ronaldo does not have a good day", Heynckes, who coached Madrid to Champions League glory in 1998, said. "As things stand now, I am coach until 2019".
Former Borussia Dortmund coach Thomas Tuchel had already turned down Bayern and is expected to be the next coach of Paris Saint-Germain.
A host of top coaches have been linked with the Bayern job. Other reported candidates included RB Leipzig's Ralf Hassenhuttl, Hoffenheim's Julian Nagelsmann and Freiburg's Christian Streich.
Both Frankfurt and Bayern had last week denied that Kovac was on his way to Munich.
Heynckes returned in an interim capacity - his fourth time in charge of Bayern, with the previous three reaping a Champions League title as well as four Bundesliga crowns and a DFB-Pokal - in October 2017 after Carlo Ancelotti was sacked.
After honing his coaching skills as a youth and then assistant coach at Red Bull Salzburg, Kovac managed the Croatian national team to the 2014 World Cup in Brazil before accepting his first club appointment at Eintracht Frankfurt.
Information from Bayern Munich correspondent Mark Lovell was used in this report.