The striker's statement against racism came just 24 hours after his former Paris Saint-Germain team mates walked off the pitch in protest against alleged racism from the fourth official in their game against Basaksehir on Tuesday.
Choupo-Moting's goal sealed a comfortable victory for Bayern, handing the defending champions the fifth win of their title defence this season.
With Group A already won and nothing at stake for Bayern, coach Hansi Flick left the likes of Robert Lewandowski, Kingsley Coman and Serge Gnabry on the bench against bottom side Lokomotiv.
Canadian winger Alphonso Davies also returned to action for the first time in six weeks, playing 69 minutes in his first appearance since tearing his ankle ligaments in a league win against Eintracht Frankfurt at the end of October.
Thomas Mueller hit the side netting while both Leroy Sane and Douglas Costa tested Lokomotiv goalkeeper Guilherme in a slow first half.
Having replaced Mueller at half-time, Gnabry injected some verve into Bayern's attack and forced a fine reflex save from Guilherme shortly before the hour mark.
Centre-back Niklas Suele finally broke the deadlock several minutes later, towering above the Moscow defence to head in a Douglas Costa corner and score his first goal of the season.
Choupo-Moting doubled the lead ten minutes from time, sending Bayern into the knockout stages with a predictable win.
Standout matches today