The Ivorians took the lead when Benjamin Henrichs deflecte the ball into his own net in the 67th minute as he was put under pressure by Youssouf Dao.
A superb free kick from substitute Eduard Lowen from the edge of the area saw the Germans draw level just six minutes later but it was not enough for his side.
Ivory Coast will find out their opponents for Saturday’s quarter-final later on Wednesday when the winners of Group C are decided.
The Ivorians have AC Milan’s Franck Kessie, Turky-based Max Gradel and Manchester United’s Eric Bailly as their overage players.
In their other games Ivory Coast beat Saudi Arabia 2-1 and drew 0-0 with Brazil, who finished top of Group D.