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The 34-year-old African legend was dropped to the bench in the Elephants' second group game, the 3-0 win over Tunisia, before returning for what was, in effect, an Ivorian reserve team in the closing 2-2 draw with Algeria.
Captain Drogba, at his Nations Cup swansong, led the Ivorian attack at the expense of Anzhi Makhachkala striker Lacina Traore.
Goalkeeper Boubacar Barry, Manchester City midfielder Yaya Toure and in-form Arsenal goal poacher Gervinho returned after being rested in the 'dead' game against Algeria.
For Nigeria, midfielder Fedor Ogude was suspended, with goalkeeper Vincent Enyeama wearing the captain's armband as its normal owner, veteran defender Jospeh Yobo, was on the bench.
Yobo has been struggling to shrug off a knock picked up in the Super Eagles' opening 1-1 draw with Burkina Faso.
The winners of this quarter-final will meet Mali in Wednesday's semi-final in Durban.
Boubacar Barry, Emmanuel Eboue, Didier Zokora, Souleman Bamba, Siaka Tiene, Koffi Romaric N'Dri, Cheikh Tiote, Salomon Kalou, Yaya Toure, Gervinho, Didier Drogba (capt)
Coach: Sabri Lamouchi (FRA)
Vincent Enyeama (capt), Efe Ambrose, Kenneth Omeruo, Godfrey Oboabona, Elderson Echiejile, Sunday Mba, John Obi Mikel, Ogenyi Onazi, Emmanuel Emenike, Brown Ideye, Victor Moses
Coach: Stephen Keshi
Referee: Djamel Haimoudi (ALG)