Prolific Pole Lewandowski became the first player to score 21 goals in the first half of a Bundesliga season with a seventh-minute opener in Sunday’s contest.
Bayern were coasting until substitute Nils Petersen caught the hosts cold just after the hour but the ever-reliable Muller side-footed home to restore the lead.
Petersen was denied another dramatic equaliser by the crossbar in injury time as Bayern, who followed a 3-2 loss against Borussia Monchengladbach with a shoot-out loss to second-tier Holstein Kiel in the DFB-Pokal on Wednesday, ultimately made it over the line.
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Freiburg had already lost Baptiste Santamaria to injury and survived a VAR scare by the time Muller teed up Lewandowski to clinically fire home at the end of a slick Bayern move.
Serge Gnabry twice tested the waters either side of Roland Sallai scuffing wastefully wide for Freiburg, while Leroy Sane – who replaced the injured Gnabry after 28 minutes – should really have hit the target with an edge-of-the-box effort.
Lewandowski saw a close-range effort deflected onto the crossbar just before the hour with Leon Goretzka’s follow-up parried to safety.
Freiburg equalised from nowhere shortly after when Petersen stooped low to head Nicolas Hofler’s flick-on over the line just 16 seconds after coming on as a substitute.
Parity did not last too long, though, as Muller coolly swept home into the bottom-right corner with 16 minutes remaining.
Lewandowski was denied one-on-one by visiting goalkeeper Florian Muller and the hosts’ profligacy almost proved costly when Petersen smashed an effort against the woodwork in the additional minutes.
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