Extra-time time beckoned Abidjan before Bayo powered home a header to break Equatorial Guinea hearts.
Equatorial Guinea had to play most of the second half with 10 men and missed a penalty when AFCON top scorer Emilio Nsue hit the post from the spot.
They looked set to force an extra 30 minutes but Bayo struck with the last kick of the game to book Guinea a spot in the quarter-final, where they will play either Egypt or DR Congo.
Equatorial Guinea were reduced to 10 men early in the second half when Federico Bikoro was shown a straight red card after catching Bayo in the ribcage with a high boot.
Mohamed Bayo wins it for Guinea in the 98th minute! 🇬🇳 pic.twitter.com/SzoY963Uxu
— Sky Sports Football (@SkyFootball) January 28, 2024
The 10 men of Equatorial Guinea won a penalty when Iban Salvador was fouled in the box but Nsue fluffed his lines and Guinea won it deep in stoppage time.