All four previous Group D 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 Ivory Coast 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.
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.
Guinea were controversially awarded a spot-kick in the 13th minute when referee Mohamed Said Kordi ruled that Ibrahima Traore's shot was handled by Salif Coulibaly.
The drama continued as, from the next attack, Baissama Sankoh blocked Modibo Maiga's shot with his hands and Mali had the opportunity to level from the spot.
Mali deservedly levelled two minutes after the break as Diaby hung up a perfect cross to the back post from the right and Maiga was on hand to power his header into the unguarded goal.
The leveller gave Mali added impetus and Yattara showed good reactions to push Mamoutou N'Diaye's low drilled effort for a corner, with Yatabare scooping over the crossbar from the set-piece.
Michel Dussuyer's side produced little going forward and they were once more let off the hook when the unmarked Molla Wague flicked a header wide in the 76th minute.
The decisive goal never came, though, meaning the fate of both teams is now out of their hands.
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