His pass split the defense, Gnabry sprinted onto the ball and fired past Leverkusen goalkeeper Lukas Hradecky to make it 2-0 at the break.
Serge Gnabry (R) scores the second goal for FC Bayern Munich during the DFB Cup final match at the Olympic Stadium in Berlin, Germany, July 4, 2020. /VCG
"We are so happy that we got the double. In the first half we had the game completely under control," said Gnabry.
With players' calls echoing around the near-empty terraces of the cavernous stadium, where Germany head coach Joachim Loew was one of a handful of guests, the game was played in an eerie atmosphere.
"It's a bit of a sad moment," admitted Bayern forward Thomas Mueller, who lamented the lack of fans, after winning the German Cup for the sixth time in his career.
"If the fans are missing at such a cup final, it's not the same."
"We've done well this season over long stretches, but it also hurts a bit."
Having skied a shot at goal moments earlier, Lewandowski made it 3-0 when he controlled a clearance kick by goalkeeper Manuel Neuer and tried a long-range speculative shot at Hradecky.
The Leverkusen keeper parried the shot, but watched in horror as it rolled behind him and over the goal line on 59 minutes.
Bayern Munich's Polish forward Robert Lewandowski scores the 1-4 goal past Leverkusen's Finnish goalkeeper Lukas Hradecky during the German Cup final football match at the Olympic Stadium in Berlin, July 4, 2020. /VCG
"I noticed that the goalkeeper was a bit off his line, so I thought I'd just give it a try," revealed Lewandowski.
"It was a little surprise it went in, but you always have to try."
It fired life into Leverkusen, whose center-back Sven Bender slipped his marker Leon Goretzka and headed home on 64 minutes.
Leverkusen nearly got a second moments later when Kevin Volland and Havertz both failed to connect with a cross.
Lewandowski claimed his second when he fired home Ivan Perisic's pass on 89 minutes.
Bayern defender Alphonso Davies conceded the penalty in the fourth minute of added time which Havertz converted just before the whistle.
(Cover image: Bayern Munich's players celebrate with the trophy after winning the German Cup final match at the Olympic Stadium in Berlin, July 4, 2020. /VCG)