The Chelsea midfielder was unable to train in Dusseldorf and coach Joachim Loew has confirmed he will not lead the team out in Gelsenkirchen.
'Michael Ballack will not play,' said Loew. 'He has a sprained knee and, after consulting with the doctor, I have decided that he will not play.
Better safe than sorry: Ballack will play no part against the Ivory Coast
'He couldn't train last week and we did not want to take any risk with our captain.'
The national team trained for the first time on Monday following Sunday's funeral for Robert Enke, who died last Tuesday.
The players were sent home on Wednesday and met up again on Sunday for the ceremony inside Hannover's Niedersachsen Stadion.
Saturday's planned friendly against Chile in Cologne was called off as a mark of respect for the 32-year-old and Loew praised the squad for the way they had handled the news of Enke's death.
Mourning: Ballack and team-mate Per Mertesacker carry flowers to Enke's coffin
'I have got to thank the team for their behaviour in these difficult hours,' he said on the website of the German Football Association. 'There was no sense in playing the game in Cologne. It was important to stop and have peace and quiet to mourn.'
The national team will pay its final respects to Enke with a minute's silence before Wednesday's game while pictures of Enke's life and career will be shown on the big screens at the Arena AufSchalke and the players will wear black armbands.
'One of Robert's shirts will be on the bench,' added Loew. 'Robert Enke was not only an extraordinarily good goalkeeper, but also an extraordinary person.'
Germany tries to move on after Enke is laid to rest in heartbreaking ceremonyGermany mourn as thousands attend memorial service for Robert EnkeGermany legends among the 45,000 mourners in tribute to EnkeGermany cancel Chile friendly after depressed keeper Enke's suicideWhy did it have to end this way? Robert Enke's suicide leaves Germany in a stunned state of mourningCHELSEA FC