The striker limped out of the action with the problem after just 18 minutes of that first leg having opened the scoring and was sidelined for Saturday's FA Cup win against Southend.
Dimitar is out alongside Ledley King (foot) and Teemu Tainio (ankle) but Martin Jol reports that 'everyone else is okay' as we travel to the Emirates with the semi-final standing at 2-2.
"We are not in bad shape," said Martin. "Dimitar Berbatov, unfortunately, is still out but is running and has done some cardio work. Michael Dawson has got an infected toe but is 99 per cent and will be involved.
"Ledley King is still out but I am still positive about him and Teemu Tainio is doing fitness sessions with our coaches and won't be involved.
"We had players back in the team on Saturday like Paul Stalteri and Jermaine Jenas for the first time in a long while and, after the first game, it can be a bit difficult to play again straight away. I have talked about it with JJ, hopefully he will come through it and it was very positive that he was back in the team."
As for the game, Martin is positive. "We will go for it because we want to win and be in the final.
"You can't say there is nothing to lose because there is a final at stake, but it is a one-off game for now away from home. They did well at our place to draw 2-2 and we now have to score goals and try to win this game. We will do everything in our power to do that."
Dimitar Berbatov will miss the Carling Cup semi-final, second leg at Arsenal on Wednesday night with the groin injury he picked up in the first leg last week.