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The hosts were dominant from the off, winning a corner within the first minute of the game, but despite being gifted plenty of space by their opponents, Pep Guardiola's charges weren't too incisive in these early stages.
On the quarter-hour mark, however, Freiburg came within a whisker of opening the scoring when Christian Gunter drove a shot towards the Bayern goal, only for Rafinha to thwart the opportunity with a last-ditch block on the goalline.
As the game went on, the home side finally got into gear and began to launch chance after chance against their relegation-battling opponents, with Thomas Muller and Arjen Robben firing just wide, and Mario Gotze and Xabi Alonso forcing smart saves from Roman Burki.
Bayern were duly rewarded for their dominance just four minutes before the break when Franck Ribery's headed flick-on to Robben, following some great play by Alonso, was coolly fired home by the Dutchman from close range.
It could have been even better for the dominant hosts as, just moments later, Muller's clever flick smashed off the post, but Freiburg survived the half having conceded the once.
Muller did eventually manage to get onto the scoresheet only a few minutes after the restart as he seized on Juan Bernat's rebounded strike to tap into the Freiburg net for his side's second goal.
Just before the hour, the World Cup winner then glanced a header just wide from close range following Ribery's cross, before the Frenchman then set up Dante, who also came close to adding a third.
Bernat could have had a hat-trick were it not for bad luck with the woodwork and some inspired saves by Burki, but despite Freiburg working miracles to keep the score down, Bayern were nevertheless able to secure all three points.