Spot-kicks were required to settle a poor round-of-16 showdown after a goalless 120 minutes at Limbe Stadium on Wednesday, and Sacko's tame strike was decisively kept out by Jesus Owono.
Pablo Ganet had passed up the chance to win it for the underdogs when Ibrahim Mounkoro denied him from 12 yards after Mali duo Massadio Haidara and Hamari Traore failed to convert, but Sacko's miss sealed a last-eight meeting with Senegal for Equatorial Guinea on Sunday.
Mali were awarded a penalty late in a drab first half when Josete Miranda was adjudged to bundled Moussa Doumbia over, but referee Bakary Gassama overturned his decision following a check on the pitchside monitor.
The Eagles had been the better side to that point and Mohamed Camara should have put them in front after the break, blazing high over the crossbar from 12 yards out after Yves Bissouma had set him up.
Neither side really looked like winning it in extra time, but it was Equatorial Guinea who were celebrating despite Emilio Nsue blazing the first spot-kick high over the bar and Ganet also fluffing his lines.
Mali claimed Owono had come off his line before Sacko struck the decisive penalty, but their protests were waved away.