Aubameyang suffered the ignominy of being substituted as a substitute against City in Thursday’s 1-0 Premier League defeat at Stamford Bridge.
The striker came on for Raheem Sterling after five minutes but toiled for an hour before he was replaced by Graham Potter after 68 minutes with youngster Omari Hutchinson.
Aubameyang looked furious as he walked off the pitch and he was not in the Chelsea matchday squad for the FA Cup third-round tie at the Etihad Stadium.
Chelsea said the 33-year-old was left out due a minor injury.
Aubameyang has endured a difficult time since joining Chelsea from Barcelona in a deal worth around £10million last summer.
Speaking after the defeat to City on Thursday, Potter said: “He put in an absolute shift for us. I thought he did everything he could for us. He was fatiguing a bit... It was a normal reaction [to being sub substituted].”