The England international looked to have tweaked the muscle in his leg when defending against the Blues' left-back Ryan Bertrand, but played on for five minutes until he was forced off.
And Wenger revealed that the injury could be one that rules him out for the last three games of the season, against Stoke, Norwich and West Brom.
"Theo looks to have a serious hamstring [injury]," Wenger told reporters. He wanted to stay on. It will be tough to come back this season."
Wenger was disappointed not to win the "strange" game, after his side enjoyed the better chances, striking the woodwork through both captain Robin van Persie and defender Laurent Koscielny.
"[It was a] strange game," he added. "They decided to lock the game up and catch us on the break. On that front, especially with the two wide players, they tried to get over the top of our full-backs an waited for us in their half of the pitch.
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"We were not quick enough with our passing today to open them up. Therefore, you always felt the game was a bit difficult. We lacked a bit of a spontaneous aspect in our game. But we still had chances to win the game, and they had zero. They had none.
"We certainly had the better of the chances because I can't remember them having one clear-cut chance. I expected the game to be very open because they had to win and we had to win but that shows you how unpredictable football is."
Wenger admits that he does not know what the result does for the Champions League places, with rivals Tottenham in action later on Saturday evening, and stated that his team hadn't fully moved on from the shock 2-1 home defeat to Wigan.
He said: "I don't know what it does for the Champions League places. It depends on results over the weekend and over the next three games.
"I don't think the result on Monday night [against Wigan] had been completely digested. At least today we didn't lose, and that solid defensive base is something we can use to have a strong finish."