Tomiyasu came on as a substitute against the Swiss side with just over a quarter of an hour to go, but was then forced to come off two minutes before the end.
Arsenal manager Mikel Arteta was unsure exactly what the injury was after the Europa League game, which Arsenal won 1-0, but he suggested it was a muscular issue.
Japan will be nervously waiting on news over Tomiyasu, who earlier this week was named in their final 26-man squad for the World Cup in Qatar.
The full-back is due to be assessed by Arsenal in the coming days and is also a doubt for Sunday’s trip to Chelsea.
“We don’t know yet,” said Arteta on Thursday night, when asked about Tomiyasu’s injury.
“He felt something and we didn’t want to take any risks. With the amount of games that we’re playing, it’s part of it.
“It can happen in training, it can happen in games and unfortunately it happened to Tomi today. The rest of the players have to be ready because we’re going to need everybody now.”