The international break limited Bayern to a makeshift side, but it comfortably came through a tie postponed until Friday to allow the club to recover from last season's Champions League triumph.
Free transfer signing Choupo-Moting was among those to get his chance and the striker opened the scoring midway through the first half before having a hand in Thomas Muller's penalty.
Duren, the designated home team who decided not to host the fixture, were certainly not embarrassed at Allianz Arena but Choupo-Moting's excellent second sealed victory for the Bundesliga champion.
The minnow had openly targeted simply bettering Barcelona and Schalke by conceding fewer than eight goals, yet it almost struck first as Marc Brasnic nodded straight at Alexander Nubel - another of four Bayern debutants in the starting line-up - after just 23 seconds.
Chances predictably followed at the other end, though, and Choupo-Moting twice might have scored before stabbing Bouna Sarr's square ball past Kevin Jackmuth for the opener.
The former Paris Saint-Germain forward then won a penalty from Joran Sobiech after Jackmuth's poor clearance, allowing Muller to get on the scoresheet from 12 yards.
A sublime Douglas Costa run and shot was met with an equally good save from the goalkeeper, who also kept Choupo-Moting at bay after half-time.
The officials were next to deny Bayern as Choupo-Moting's delicate finish appeared to cross the line before David Putz headed clear, then Jamal Musiala's mazy dribble concluded with a low shot against the post.
Bayern's new striker persisted, however, and turned on the edge of the box to rifle a right-footed shot into the top-left corner and complete the scoring, although there should have been a fourth when Javi Martinez nodded against the upright.