Muller found himself out of favour at times under Carlo Ancelotti and there had been speculation he could exit the Allianz Arena.
Heynckes is now in charge of Bayern for the fourth time in his managerial career and the clash with Freiburg in Munich on Saturday will be his first since replacing Ancelotti.
Muller was a key man under the 72-year-old during his last spell at the Bayern helm as they claimed a treble, including the Champions League, in 2013.
Heynckes has indicated the Germany international will be a vital member of his squad going forward while he is also ready to rely on Arjen Robben and Franck Ribery, who were also members of his squad in 2013.
He said: "Football is played with the legs, but on the other hand the head is far more important for a few.
"I've rarely seen someone as emotional as Robben was in his last Netherlands match. It shows that his enthusiasm is still burning.
"This also applies to Ribery. He's already back in the weight room and I am convinced he will do well under me.
"I had a longer chat with Muller, and I've seen him in training this week. He's just like in the old days in front of goal."