Manager Sam Allardyce said: "It is a serious injury. You could see by the way that Khali went down and stayed down he was in trouble.
"He was a big loss because he was the major player for us, opening up Wigan. If he had stayed on more and more chances would have come our way."
Striker Kevin Davies also suffered an ankle injury as Bolton failed to build on a goal from Stelios Giannakopoulos after 63 minutes.
Allardyce felt Bolton were unlucky to be penalised for N'Gotty's challenge on Johansson that led to a free kick being awarded, which ultimately led to the Wigan equaliser.
The Bolton boss said: "It wasn't a foul as far as we are concerned but we should have defended it better. It wasn't a great first shot.
"But the players in the wall didn't do their job properly and Jussi couldn't push it to one side.
"It was disappointing but the squad put in a tremendous effort considering the number of players we are without.
"We managed to take the game to Wigan as best we possibly and got our noses in front.
"I just hoped for their benefit we could have won this game 1-0, having just slipped up at Portsmouth.
"It was a spirited show from us against Wigan after a very good start. But fatigue did set in again and that's why we have drawn two instead of winning the last two matches."