Choupo-Moting scored for the sixth game in a row with a brilliant long-range strike in the second half to hand Bayern a comfortable win in Munich.
Victory made it six wins in six games in the group stage for Bayern - the second time in a row and the third time in four years they have achieved the feat.
With Bayern already group winners and Inter safe in second place ahead of kick-off, both coaches rested several star players for what was essentially a dead rubber fixture in Group C.
Yet the game still fizzed in the opening minutes, as both keepers were tested by stinging, long-range efforts from Joshua Kimmich and Nicolo Barella.
Inter were annoyed not to be given a penalty early on after Sadio Mane appeared to block a Barella shot with raised arms.
Bayern had another lucky escape later in the first half when Lautaro Martinez scooped a Robin Gosens cross over the bar from point blank range.
But the hosts slowly wrestled back control and took a deserved lead from a corner just after the half-hour mark.
Martinez once again cut an unfortunate figure as he slipped in the box to allow Benjamin Pavard to rise unchallenged and head in the opener.
Choupo-Moting found the net with an elegant overhead kick after the break, but the goal was ruled out for offside.
The veteran striker remains in irresistible form, however, and there was no stopping him as he rifled Bayern's second into the top corner on 73 minutes.