Leon Goretzka put Bayern ahead with half an hour gone at Munich's Allianz Arena before Robert Lewandowski bagged his 13th Bundesliga goal this season to make it 2-0 with 15 minutes left.
Bayern have now scored 100 goals this calendar year, one short of the record for a German club, set when Cologne netted 101 times in 1977. Freiburg substitute Janik Haberer caused a few nervous looks in the Bayern ranks when the visitors finally beat Manuel Neuer in stoppage time.
In Munich, goal-scorer Goretzka praised Neuer who repeatedly denied Freiburg with a string of top-class saves. "When you walk out onto the pitch with him in front of you, it is something special - you have 100 per cent trust in him. "He is a absolute machine and has been world-class for years.".