Freiburg was the sole team yet to taste defeat in the league this season, but it was always second best against Julian Nagelsmann's side on Sunday (AEDT).
Leon Goretzka opened the scoring on the half hour and Bayern saw several chances to pad its lead go begging.
But Robert Lewandowski could hardly miss as he eventually made it 2-0, Bayern at least temporarily going four points clear of Borussia Dortmund in second despite Janik Haberer's late consolation.
Freiburg's defence had conceded only seven goals going into this game, but Bayern found consistent joy in carving a way through the backline.
Alphonso Davies was a menace down the left and forced saves from Mark Flekken twice in the opening six minutes before Lucas Holer could have put Freiburg ahead.
Holer should have done better as he fired wide and, after some fruitless probing from Leroy Sane, Goretzka punished Freiburg's earlier profligacy with a confidently taken close-range finish at the end of another well-worked Bayern attack.
Only the right-hand post denied Goretzka a second as Bayern upped the ante in search of a second after the interval, with Sane then lashing over on the volley.
It was Sane who supplied the final pass as Lewandowski put the game beyond doubt.
The Poland international tapped in from point-blank range after Sane had combined with Kingsley Coman, but there was late consolation for Freiburg, whose reward for a strong finish came in stoppage-time as Haberer wriggled free in the box and beat a frustrated Manuel Neuer.