The former Gabon international scored two goals in six group stage appearances but has been cut from the squad while January signings Mykhailo Mudryk, Enzo Fernandez and Joao Felix have been added.
Aubameyang was also not included in Chelsea's matchday squad as they drew goalless against Fulham on Friday, with David Datro Fofana preferred to start from the bench.
The 33-year-old has only scored three goals in 17 appearances across all competitions since moving to Stamford Bridge from Barcelona at the start of the season.
Despite deciding to leave out his only fit recognised centre forward, Potter says he has nothing against the former Arsenal captain.
"I don't think it's going to be difficult because Pierre is a professional. He was the one that missed out, he's done nothing wrong at all," Potter said after Friday's match.
"We wanted to give David some time today. Whichever decision there was always going to be a debate. It was my decision, a tough decision."
He added: "Nothing bad against him I understand his disappointment but I've got a responsibility to make these decisions and articulate them to the player. He handled it well and trained well today... Yes [he can fit in the system], everything is up for grabs and needs to train like today. Everything is up for grabs."
Aubameyang will look to get back into the squad when Chelsea face West Ham United in their next game.
