The Germany international, linked with an imminent move to the English Premier League, was out of action for more than a year before his comeback in December.
"I hope that Ilkay can make it. But we will have to wait and see. He will definitely play again for us this season," Dortmund coach Juergen Klopp told reporters on Monday.
Klopp, who will be leaving Dortmund at the end of the season after seven years in charge, also hopes midfielders Sebastian Kehl and Kevin Grosskreutz could be fit after injury problems.
Dortmund are desperate to win the Cup to secure a Europa League spot next season and rescue something from a disappointing campaign.
If Dortmund beat Bayern and VfL Wolfsburg overcome third-tier Arminia Bielefeld they could even advance to the Europa League if they finish seventh in the Bundesliga.
Understandably, Klopp was in no mood for nostalgia.
"I don't sense any end-of-an-era feeling," Klopp said. "We do not only want to reach the final but we want to win that thing.
"If you want to win the Cup then you have to get past Bayern at some stage. That's the way it goes."
Dortmund lost last season's final to Bayern after beating them in the 2012 edition. They also lost both league games to Bayern this season.
"This is game is about everything and we have to know that we have been (against Bayern) an uncomfortable opponent. I have the feeling that we are not without a chance against them.
"We cannot allow ourselves to be passive against them. We have to be active the entire game and not just set occasional markers," Klopp said.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
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