Michel Dussuyer's side will confront Ghana on Sunday emulating the draw at a Malabo inn.
Guinea and Mali had completed level in Group D after they drew every one of the three pool matches 1-1.
It is the first run through parts have chosen a group's capability in the competition since 1988, when Algeria benefitted at Ivory Coast's cost.
This time, Ivory Coast completed top of Group D in Equatorial Guinea in the wake of beating Cameroon 1-0 - the main match in the gathering not to complete in a 1-1 draw.
Mali's football affiliation president Boubacar Diarra went first and hauled out the ball that put them third in the gathering.
With Diarra in tears, Amara Dabo, monetary executive of the Guinea sports service, then drew the ball that affirmed his side in second place.
Dabo said: "The lord of football fortune has grinned upon Guinea after this hard long excursion."
Previous Mali worldwide and ex-Tottenham and West Ham striker Frederic Kanoute, 37, communicated his bafflement at the attracting of parcels to choose who experienced.
He tweeted: "This is no more game. Be that as it may boldness to our Guinean siblings."
Guinea mentor Dussuyer and Mali manager Henri Kasperczak had additionally both said before Thursday's draw that it was an unreasonable method for differentiating the groups.
"Mali don't should be disposed of thusly, pretty much as we don't," Dussuyer said.
Kasperczak included: "We need to take care of the issues of capability without a drawing of parts."
The Confederation of African Football (Caf), which composes the competition, said that option frameworks to independent groups would be considered in future.
Caf media chief Junior Binyam said: "We need to remain by the regulation additionally consider how we enhance it.
"It's not reasonable to have a group going out like this. It truly is the most exceedingly awful choice - to need to settle on a choice along these lines - in light of the fact that everyone expected it would be chosen the field."
At Euro 2008, Uefa had decided that Turkey and the Czech Republic - who went into their last gathering match against one another with indistinguishable records - would have been differentiated by a punishment shootout had they drawn. Turkey won the match 3-2.