After the two nations played out three 1-1 draws in their respective campaigns in Group D in Equatorial Guinea - including against one another on Wednesday - the rarely-used tie-break will take place on Thursday at a hotel in Malabo at 15:00 GMT.
Group C winners Ghana awaits the side who progresses to the quarter-finals but both Mali coach Henri Kasperczak and Guinea tactician Michel Dussuyer slammed the tie-break method - claiming it was unfair on the team who exits.
"We have to solve the problems of qualification without a drawing of lots," Kasperczak said.
"You have to respect the rules, we have no choice. We are going to be nervous, Guinea also.
"We must find a more sporting way, fairer. This does not correspond to a sporting spirit."
Dussuyer said: "Mali do not deserve to be eliminated in this way, just as we do not.
"Mali didn't lose a game - they played very well in the tournament.
"I would be disappointed but it's hard for any team. No-one deserves to be eliminated."
Guinea's Ibrahima Traore suggested an on-field way of deciding who advances, after both sides finished level on goals scored, conceded and head-to-head record.
"It's not fair for both teams - I don't make the rules but we could do it on penalty kicks or extra time," he said.
"The team who deserve to win would do it on the pitch. Not like Thursday.
"We and Mali will be really anxious because we don't know if we go home or stay and it's not up to us. It'll be really difficult to sleep - it's not a good situation."
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