Muller was sent off in Bayern's final group match in December when, in attempting to bring down a high ball, his high boot caught Ajax defender Nicolas Tagliafico on the back of the head.
The Germany worldwide apologised to Tagliafico following the incident and has now been handed his punishment by UEFA.
Bayern plays at Liverpool on February 19 and hosts the second leg on March 13 in a clash of five-time European champions.
The sending-off was the first of Muller's career and after the incident he posted on social media: "I would like to apologise to Nico Tagliafico for the incident".
'There was no intention [in the foul]. "It was unintentional. Get well soon".
He also told reporters after the match that Spain were "rude on the pitch" and bad losers.