Second-placed Leipzig crashed to a 1-0 defeat at home to Wolfsburg where Germany's Mario Gomez scored the victor while Dortmund lost 2-1 away to Hertha Berlin.
If you don't take your chances, Bayern will punish you.
Carlo Ancelotti's men continued with their clinical chance conversion after the restart as Lewandowski sealed his brace to score his 21st goal of the season putting the result beyond doubt in the 55th minute.
Lewandowski converted Mueller's pass on 38 minutes, then Douglas Costa added a second three minutes later to put Bayern 2-0 up at the break.
Frankfurt had given as good as they got in the first half, with Ante Rebic going close before Mats Hummels was forced to make a goal-saving tackle to deny Branimir Hrgota an easy finish.
Frankfurt's troubles were compounded when captain Makoto Hasebe, the league's most capped Japanese player with 236 appearances, was taken to hospital for stitches to a cut on his shin. Last week, Leipzig came away from Augsburg with a 2-2 draw and missed a chance to keep pressure on Bayern Munich.
The match also saw Bayern defender Jerome Boateng return from a four-month injury lay-off as he appeared as a second-half substitute for Javi Martinez.
In Leipzig, second-placed RB crashed to a 1-0 defeat at home to Wolfsburg as Germany's Mario Gomez scored the victor.
Gomez, who played under Jonker in his five games as interim coach at Bayern, has 11 goals in seven games with the Dutchman in charge.
Despite the defeat, Dortmund stay on third place whereas Berlin continue on fifth place of the standings.
"In the second half we were better and controlled the game well".
Borussia's Pierre-Emerick Aubameyang scored for the eighth time in four games to remain the league's top-scorer - one ahead of Lewandowski - with 22 goals, but could not prevent defeat.
Marvin Plattenhardt dashed Dortmund's hopes, however, thundering a 71st-minute free kick into the top corner to leave Dortmund stuck on 43 points in third place and Hertha closing in on 40 in fifth.
Heimes, who founded a charity for children with cancer, was a motivating factor in Darmstadt's promotion in 2015.
Julian Nagelsmann's side could have been further clear of the capital club, but they had to settle for a share of the spoils from a 1-1 draw at Freiburg.
Ingolstadt was hosting Cologne for the late game.