The Gunners managed another impressive performance as they bested Newcastle United 3-0 at home on Monday.
Aubameyang, who scored two goals, was taken off with ten minutes to go.
The Gabon striker went right down the tunnel, but Arteta says it was due to illness not an injury.
"Yeah, he had to go in and we decided to change him," he told reporters.
Arteta mentioned "stomach issues" that were bothering Aubameyang, who appears back to his best form after a slump in the first part of the season.