Mohamed Bayo headed in the 98th-minute send Guinea to the quarter-finals of the Africa Cup of Nations.
Equatorial Guinea midfielder, Federico Bikoro was dismissed 10 minutes after the break for catching Bayo in the ribs with his studs.
The National Thunder were awarded a spot-kick midway through the second half after Sekou Sylla caught Iban Salvador, but captain Emilio Nsue, who is the current highest goal scorer with five goals hit the base of the right-hand upright.
With the game set to head to extra time, striker Bayo head home Ibrahim Diakite’s cross from the right flank just inside the near post in the final minute of added time.
The West Africans will face either Egypt or DR Congo in the last eight in Abidjan on Friday, and will find out the identity of their opponents when those sides meet later on Sunday.