The two teams could no be separated after 90 minutes on Wednesday, as Modibo Maiga's second-half strike cancelled out Kevin Constant's 15th-minute penalty for Guinea.
The result means that both sides are locked on three points in Group D, with the same goal difference and the same goals for and against totals, having drawn both their previous games 1-1 as well.
The Confederation of African Football (CAF) will now draw lots to determine who follows Ivory Coast into the last eight, setting up a meeting with Ghana on Sunday.
Herve Renard's men booked their spot as group winners with a 1-0 victory over Cameroon at Nuevo Estadio de Malabo, thanks to Max Gradel's 36th-minute strike.
Had that clash also ended 1-1 all four sides would have involved in the drawing lots in order to determine who progressed.
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