Arteta decided to start Alexandre Lacazette at Goodison Park, with Arteta explaining he wanted to freshen up his forward line with Aubameyang without a goal in his last five.
He said: "We made some changes today, we have to freshen up. We have some games coming up and I want to have everyone fit and available."
Aubameyang came on with just five minutes remaining and was on the pitch when Demarai Gray scored a stunning winner for the Toffees.
Everton came from behind to earn all three points after Martin Odegaard gave the visitors a first half lead.
Moments after Gray’s goal, Aubameyang had the chance to rescue a point for his side, but spurned an injury-time strike wide of the post.
Following the defeat, Sky Sports pundit Neville suggested that trouble could be brewing between manager and player, particularly after Eddie Nketiah was called upon first.
“I think there will be a problem with Aubameyang off the back of this game. I don't think he'll like Nketiah coming on [before him], I don't think he'll like being sub full stop,” Neville said.
“I think when [the late chance] comes, he makes a good run outside, it's one of them that is hard to play as a side foot over to that corner, you almost want to guide it in with your left into that far corner. It's a little awkward and unnatural in terms of how he's tried to finish it.”
Aubameyang was a late sub, with Alexandre Lacazette preferred
Neville then predicted that a move could be on the cards for Aubameyang, claiming that both parties would be open to an exit.
He added: “There's always that little bit of a bug between him and Arteta. I know he's the captain, but he leaves him out, and it just feels like it's going to be a little bit awkward.
“I think it's gonna cause a problem. I suspect if he could get money for him and get someone else, he would, and I think if Aubameyang could move on, he would.
“It could maybe turn a little sour.”