Kovac also has the chance to secure a domestic double when the Bavarians face off with RB Leipzig in the DFB Pokal final on May 25.
After their triumph Kovac addressed the rumours surrounding his dismissal, which the club have also denied.
“I am convinced I will continue,” Kovac told Sky, also saying he had “other first-hand information” he would remain at the Allianz Arena next season.
Kovac was serenaded by the Bayern fans as their title was assured and offered his gratitude to the supporters.
“That touched me, because I am a human being of flesh and blood,” the 47-year-old continued.
“I want to thank the whole crowd.”
The coach added to reporters in Saturday's press conference: "I talk to my bosses, as you know I have three of them. And when you talk with each other you can hear in which direction things will go.
"I think I interpret things the right way."
Kovac joined his former club, whom he represented for two seasons on the pitch, in the summer of 2018 having impressed at Frankfurt.
Bayern started the season slowly but overhauled a wobbling Dortmund team to secure the Bundesliga crown.
A source told Spox that “damaging behaviour” from the head coach has led to his position being “weakened for weeks.”
Kovac took on the speculation he might be headed for the exit earlier this week, in a press conference prior to Saturday’s game.
“These [stories] are side issues that I’m not interested in,” he said.
“We now have two tasks to focus on, we could become champions, our full focus is not on what’s being told, I’m not interested.
“I have a contract that will run for another two years and I want to fulfil that, we have developed well and we only lost twice after the Dusseldorf game.”