A David Alaba free-kick and Serge Gnabry's second put Bayern on course for victory in Berlin before Lewandowski took his tally for the season to 50 with a third just before the hour.
Sven Bender gave Leverkusen some hope but Lewandowski's second in the 89th minute put the result beyond doubt, although Kai Havertz added a penalty in stoppage time.
It was an 11th successive victory for Bayern since German football resumed following the coronavirus outbreak.
They will now hope to go on and make it a treble by winning the Champions League in August. They lead Chelsea 3-0 after the first leg of their last-16 tie.
Juventus took another stride towards a ninth consecutive Serie A title as they moved seven points clear at the top with a resounding 4-1 derby win over Torino.
Paulo Dybala and Juan Cuadrado had put the hosts 2-0 up inside the opening half-hour at the Allianz Stadium before Andrea Belotti pulled one back from the penalty spot.
It was a memorable occasion for 42-year-old Buffon who, featuring for the first time since December, made a record 648th Serie A appearance, overtaking the previous mark of Paolo Maldini.
Juventus' victory was made all the sweeter by a 3-0 home defeat later in the day for second-placed Lazio against AC Milan.
Zlatan Ibrahimovic was again on target for Milan, scoring from the spot before the break after Hakan Calhanoglu had opened the scoring. Ante Rebic added a third just before the hour as Milan climbed to sixth and dealt a heavy blow to Lazio's lingering title hopes.
At the other end of the table, Lecce's relegation fears increased as they were beaten 4-2 by Sassuolo.
Late goals from Jeremie Boga and Mert Muldur proved decisive after Lecce had twice come from behind. Fabio Lucioni first cancelled out Francesco Caputo's early opener before Domenico Berardi and Marco Mancosu traded penalties.
In Spain, Valladolid moved closer to LaLiga survival as a last-gasp Joaquin goal gave them a 1-0 win over Alaves.
Joaquin struck with just two minutes remaining at the Jose Zorrilla Stadium, earning a first win in six and lifting the side 10 points clear of the relegation zone.
Zouhair Feddal equalised 11 minutes from time as Real Betis, who had earlier had a penalty award overturned by VAR, grabbed a 1-1 draw at Celta Vigo. Nolito had opened the scoring for the hosts with a free-kick midway through the first half.
Substitute Fede Vico scored an 86th-minute equaliser as Granada snatched a 2-2 draw in their mid-table battle with Valencia.
Carlos Fernandez had opened the scoring for Granada with a 61st-minute penalty but quickfire replies from Manuel Vallejo and Gonçalo Guedes had turned the game around.