Published: 2020-08-09 03:18:37 BdST
The Bavarians, who won the domestic league and Cup double, quickly killed off the tie with a ninth minute Lewandowski penalty, after having won 3-0 in London in the first leg in February.
Bayern will be on an 18-game winning streak across all competitions as they head into next week's Final Eight tournament in Lisbon.
Polish striker Lewandowski, with 53 goals in 44 matches in all competitions this season, turned provider to set up Ivan Perisic in the 24th minute as the hosts showed no lack of fitness despite a five-week gap since their last competitive game.
Chelsea, who conceded seven goals in a two-legged European tie for the first time, got onto the scoresheet with Tammy Abraham's tap-in from a Manuel Neuer pass a minute before the break.
Bayern substitute Corentin Tolisso restored their two-goal lead in the 76th and Lewandowski headed in his second eight minutes later to make it 13 goals in the Champions League this season.