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.
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.
Mali started well as Abdoulay Diaby fired one shot over the bar and saw another blocked inside the opening 10 minutes, while Mustapha Yatabare felt he should have had a penalty after being pushed to ground by Fode Camara when chasing a long ball.
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.
Constant demonstrated supreme confidence to dink the subsequent penalty straight down the middle and hand his side the lead.
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.
However, captain Keita fluffed his lines with a weak penalty that Naby-Moussa Yattara saved low to his right.
As both teams struggled to defend on an uneven surface the end-to-end nature of the contest continued, and Maiga produced a fine fingertip save from Yattara with a fizzing 30-yard drive in the 34th minute.
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.
As the clock wound down, Mali saw tentative penalty claims for handball waved away after a bout of pinball in the area.
The decisive goal never came, though, meaning the fate of both teams is now out of their hands.
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