All four previous pool matches before Wednesday's fixtures produced 1-1 draws, meaning it was winner-takes-all in Mongomo.
However, the game ended all-square and, with Cote d'Ivoire having beaten Cameroon 1-0 in the other pool match, lots will have to be drawn to decide who joins Herve Renard's men in the last eight.
It is the first time since 1988 that this method has been used to decide the fate of two tied teams, with Algeria having gone through at the expense of Ivory Coast on that occasion.
Guinea were primed to progress following Kevin Constant's first-half penalty, with Seydou Keita missing one at the other end.
But Mali struck back shortly after half-time as Modibo Maiga levelled matters with a close-range header.
Henryk Kasperczak's side enjoyed the better of the play after the equaliser, but were unable to find a crucial goal.
