The midfielder was withdrawn in stoppage time, replaced by Thomas Vermaelen, and now faces a race against time to be fit for Arsenal's final day match against Newcastle.
"Arteta is not all right," Arsenal manager Arsene Wenger said after the match. "Arteta pulled his calf, so that could be a problem for Sunday. We don't know, we have to wait 24 hours. He will be a massive doubt for Sunday."
Though the Spaniard is likely to miss his side's trip to St James' Park, Wenger remains confident that his side can claim the victory it needs to seal a place in next season's Champions League.
"It's all open. But it depends on our result. Even third place is not out of sight if we win our game," Wenger said. "I am confident, because we have experience. Because we play for a long time now under massive pressure and have always found solutions for the problems we've faced, so I'm confident."
Wigan needed to win the match in order to keep its survival hopes alive, but after Theo Walcott's 63rd-minute goal, the Latics imploded, and Wenger believes the FA Cup winners will be missed next year.
"When we scored the second goal it was a massive blow for Wigan and they never recovered from that, and then it became a comfortable game, we scored three and four," Wenger said. "It's sad that Wigan are going down, because they are a good team. They play good football and are an intelligent team, with good players. If they stay together they will certainly come up again."