Bayern Munich head coach Niko Kovac has accepted an apology from the wife of Thomas Muller after her social media criticism of the coach's treatment of the Germany star.

Lisa Muller hit out at Kovac for leaving her husband on the bench for Saturday's 1-1 Bundesliga draw against Freiburg, in which the champions conceded a late equaliser.

When Kovac prepared to bring on the forward during the second half, Lisa Muller posted on Instagram: "More than 70 minutes until he finally has a brain wave."

Although Thomas Muller downplayed his partner's comments when he spoke to the media after the match, Bayern said on Sunday she visited Kovac to apologise.

"Lisa Muller, the wife of Thomas Muller, went directly after the Bundesliga game against Freiburg in the Allianz Arena to coach Niko and apologised for her Instagram post during the substitution of Thomas Muller," Bayern's statement said.

"Kovac accepted her apology."

Bayern are second in the league, four points behind leaders Borussia Dortmund. 

Kovac's men are next in action at home to AEK Athens in the Champions League on Wednesday.