Lewandowski put the visitors ahead six minutes after halftime but Sofiane Hanni's volley on the hour gave the Belgians, who had missed a bagful of golden chances in the first half, their first Champions League goal of the season.
France's Tolisso, however, rose high to head in a Joshua Kimmich cross in the 77th minute and leave Anderlecht bottom of the group and without a point from five matches.
Bayern are on 12 points, three adrift of Paris St Germain, who were 7-1 winners against Celtic and are the Germans' final group opponents next month.
Heynckes, who led Bayern to a treble in 2013, took over last month following the sacking of Carlo Ancelotti and quickly turned their season around.
(Reporting by Karolos Grohmann; Editing by Toby Davis)
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