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.
She posted on Instagram to her 140,000 followers: “More than 70 minutes until he finally has a brainwave."
But she hastily deleted the post and fronted up to Kovac and apologised after the game.
Bayern star Muller came out and defended her saying: "It was out of emotion. In retrospect, I don't think it was super. But she just loves me, what should I do?"
Meanwhile Kovac accepted the apology and said: "There's nothing to clarify. Obviously it wasn't Thomas himself who wrote that."
In an attempt to draw a line under the incident, keen horse rider Lisa has deleted every picture of her with her husband from her Instagram account and stopped following the World Cup winner.
The draw at home to Freiburg leaves Bayern second in the Bundesliga, four points behind leaders Borussia Dortmund.
Kovac's men are next in action at home to AEK Athens in the Champions League on Wednesday.
Then the Bavarians go to the Westfalenstadion to face Dortmund on Saturday who are unbeaten in all competitions this season.
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