Lewandowski made it 2-1 three minutes after the interval when he got ahead of Mats Hummels to head Lucas Hernandez’ cross inside the far post.
Lucien Favre reacted by bringing on 17-year-old Jude Bellingham with half an hour remaining, and then Thorgan Hazard and Julian Brandt with around 20 minutes to go. Flick brought on Leroy Sane and Lewandowski set up the former Manchester City winger to effectively seal the result on a counterattack in the 80th.
The former Germany striker scored from the spot early in the second half to tie Hans-Joachim Abel’s record in the top division. Abel scored his penalties for Fortuna Dusseldorf, Bochum and Schalke between 1973 and 1984. Kruse set up the unmarked Robert Andrich to sweep in under the crossbar in the 13th, then played Becker in for Union’s third before the break.