Muller was sent off for a poor tackle on Ajax's Nicolas Tagliafico in a 3-3 draw in December in the final Champions League group game for both sides.
Despite apologising to Tagliafico after the game, Muller is still set to serve a two-match ban after Bayern’s appeal was rejected by UEFA on Monday.
However, Kovac is confident Bayern can deal with the 29-year-old's absence for the last-16 tie, which begins at Anfield on February 19.
"I have expected it actually. A red card means you will get banned from two matches, two yellow cards are a one-match ban," he told a news conference.
"UEFA didn't want to lower a red card punishment to a one-match ban. Therefore, it is normal. I am happy the ban wasn't extended.
"Missing the games against Liverpool is quite annoying for Thomas and the team, as well.
"But if he's not able to play, someone else will. That other player will perform equally as good, so we can be successful."
Muller will likely be joined by Arjen Robben on the sidelines, with the Dutch winger having not played since November due to a thigh injury.
Goalkeeper Manuel Neuer also remains a doubt for the Champions League round-of-16 tie after injuring his right thumb.
Liverpool will also be without a star of their own, as defender Virgil van Dijk is banned for the first leg after picking up three yellow cards in the group stage.
The Netherlands international has been vital to the club’s success this season, having played in all 25 Premier League games as well as all six of their Champions League group fixtures.
However, Muller has played a similarly important role in Bayern's campaign, bagging five goals and assisting five others in all competitions.
They will be hoping star striker Robert Lewandowski can continue to deliver in Muller’s absence, with the Poland international scoring 24 times already this season.
The two sides first meet on February 19 at Anfield before a return trip to the Allianz Arena on March 13.