The Frenchman deflected the ball into his own net at the Emirates Stadium as the Gunners lost further ground in the Premier League title race.
The North London club are now six points behind leaders Chelsea with seven games left to play this season.
"I was coming back and I think the keeper kicked the ball onto my leg and it was an own goal," Flamini told Arsenal's official website.
"Of course it's very disappointing because it was a difficult game. We conceded an early goal, we didn't play a great first half but we were trying, trying, trying. But we played a great second half because we came back winning 2-1 until the end and then we were unlucky on the second goal."
Arsenal return to Premier League action on Saturday when they entertain Manchester City.