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."
After the game, both Muller and Kovac had attempted to play down the criticism.
"It was out of emotion. In retrospect I don't think it was super. But she just loves me, what should I do?" the Germany star signalled to Sky .
Kovac added: "There's nothing to clarify. Obviously it wasn't Thomas himself who wrote that."
Serge Gnabry seemed to have earned his side three points with a late goal, only for Freiburg's Lucas Holer to swoop in the 89th minute to the frustration of Kovac and his charges.
Bayern are second in the league, four points behind leaders Borussia Dortmund.