Lewandowski, last season’s top scorer in Germany, showed his class with two superb strikes at Freiburg’s sold-out Schwarzwald Stadion.
Having volleyed Bayern level in the first-half, to cancel out Freiburg’s shock early lead, the Poland hot-shot chested the ball down, flicked it off his left foot and fired home the winner off his right.
The victory leaves Bayern six points clear of second-placed RB Leipzig, who host Eintracht Frankfurt on Saturday.
“It was a hard game, we didn’t have so many chances, so we have to be happy with the three points,” said Lewandowski after the match.
“We had a bit of luck. We were a bit slow at the back, we tried everything and they defended well.
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“You have to be patient in games like that and I am just glad we got the win. It’s not easy to play in temperatures like that,” he added.
Bayern coach Carlo Ancelotti was impressed with his team’s character, not their performance.
“We played a good opponent, who invested a lot, but we simply didn’t play well,” said the Italian. “What I did like was the will and the character the team showed, but we can’t be happy with the way we played, only with the result.”
Freiburg, who stunned Bayern with a shock 2-1 defeat when the sides last met at the Schwarzwald Stadion in May 2015, took an early lead on four minutes.
“Bayern had a lot of chances, but I am not annoyed,” said Freiburg coach Christian Streich, with his team eighth. “We have to pick up our points against other teams, the boys did well and very little wrong.”
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The thermometer showed minus six degrees Celsius (21.2 Fahrenheit) in the stadium, but Freiburg were on fire in the opening exchanges.
Bayern defender Mats Hummels' mis-hit clearance fell to Freiburg's Italian Vincenzo Grifo, who played Janik Haberer into the area.
The attacking midfielder produced a stunning finish to beat Bayern goalkeeper Manuel Neuer as his shot flew into the far corner.
Freiburg enjoyed a string of half chances as Bayern looked far from sure of themselves.
The Bavarian giants, who are chasing their fifth straight German league title, drew level when Lewandowski showed his class.
Having been denied at close range when Freiburg captain Mike Frantz blocked his shot on 35 minutes, Lewandowski was not to be denied. He volleyed home the resulting corner from Douglas Costa as Bayern went into the break at 1-1.
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Nevertheless, Bayern stars Thomas Muller and captain Philipp Lahm trudged off clearly unhappy.
Things did not improve for Bayern in the second-half as Freiburg defended doggedly and tried to catch the guests on the break.
Bayern’s Costa was booked just three minutes after the interval for bringing down Freiburg’s midfielder Maximilian Philipp.
Ancelotti brought on Franck Ribery and Juan Bernat to inject some pace on the flanks for the final 20 minutes.
There were some nervous looks in the Bayern defence on 74 minutes when Haberer went down in the tackle after Hummels’ challenge. But referee Manuel Graefe spotted the goal-scorer had gone to ground and booked Haberer.
It was Ribery’s cross which led to Lewandowski’s winner and the Poland international showed a world-class finish for his 14th league goal of the season to deny mid-table Freiburg a point. He is still two goals behind Borussia Dortmund’s Pierre-Emerick Aubameyang, the league’s top scorer, who has 16 so far this season.
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