Chelsea made eight new signings in the January transfer window, including a Premier League record deal to acquire World Cup-winning midfielder Enzo Fernandez for €120 million.
However, Graham Potter could only pick three of his side's new players to feature in their Champions League campaign, which continues with a round-of-16 fixture away at Borussia Dortmund on Feb. 15.
Of the eight new signings, Fernandez, Mykhailo Mudryk and Joao Felix were included in the squad as David Datro Fofana, Noni Madueke, Andrey Santos, Gabriel Slonina and Benoit Badiashile all missed out.
"I think whichever decision we made there was going to be conversation, of course," Potter said after Chelsea's draw with Fulham on Friday. "It was a tough decision, but it was my decision. Sometimes you have to make these calls. As I said, it's absolutely nothing bad against him.
"It is difficult, it's tough because I come empathic, but it's my responsibility to make these tough decisions and articulate them as honestly and as well as I can to the player and respect the fact he is disappointed. He's trained today fantastically, which is what I'd expect. He's a top guy for us."
Aubameyang was pictured in Milan on Friday evening, hours after Chelsea's Champions League squad was announced. But Potter said he was not concerned.
"He trained today. He trained very well, and he has the weekend off so we can report on Monday. It's a free world."
He added: "I don't think it will be difficult because Pierre is a professional, and of course I understand he will be disappointed It was a tough decision, a tough call.
"We had three coming in and two had to go out, so he was the one who missed out. We wanted to give David [Fofana] some game time today and see where's he's out and give him that opportunity."
Aubameyang signed a two-year contract at Stamford Bridge when he joined the club on a deadline day deal from Barcelona in September.
The Gabon international has struggled for form since joining the Premier League club, scoring just three goals in 18 appearances. He has not started for Chelsea since the World Cup break.
Potter's side are 10th in the Premier League and are the lowest scorers in the top 10.
Information from ESPN's Connor O'Halloran contributed to this report.