The Real Madrid loanee was smacked in the face twice as Arsenal players swarmed into the corner to celebrate.
Aubameyang’s was the only goal of the game at St James’ Park, as the Gunners picked up a comfortable win in their first game of the season.
After a hectic summer transfer window, which saw Unai Emery recruit four new players, Ceballos was left on the bench for the Premier League opener.
The youngster signed on a one-year loan deal earlier in the summer, and came on as a second-half substitute in the away win.
However, he won’t have been happy after Aubameyang’s winner, as he came off worse for wear after the celebrations.
The 23-year-old midfielder appeared to take several blows to the head as Aubameyang and the rest of the team bundled into the corner flag.
He walked off holding his nose, as his team-mates walked back to the centre circle.
Ceballos impressed when he came on, as he gave Arsenal an extra spark in the centre of midfield.
And afterwards, Emery was complimentary of the way his new signings – including Ceballos had blended in with the rest of the team.
“I explained yesterday that the circumstances are different. David Luiz did pre-season with another team and he is okay to play physically but he only trained completely with us yesterday,” he said.
“On Friday he did 30 minutes with us. I was thinking to give them confidence to work together because they were working well together, Sokratis and Chambers.
“Nicolas Pepe came one week ago and physically he needs to get his best fitness to be ready to play 100 per-cent for 90 minutes. I think that today 20 minutes is good for him.
“And Ceballos is in the middle because he came before Pepe but he got an injury and he stopped training.
“But he needs to know the Premier League, so today was important for him and for us.
“I also used Reiss Nelson and Willock because they deserved to be with us and to give them confidence can help us. It’s the same with Martinelli, he played the last 10 minutes because he deserved it.”