The result also means that the co-hosts have booked their place in the quarter-finals of the tournament.
Abdoulaye Ndoye came close for Equatorial Guinea in the opening stages when his powerful effort was deflected behind for a corner.
Demba Ba should have given Senegal a first-half lead, but his side-footed shot from inside the area went wide.
Senegal continued to press as Guirane N'Daw's drive was tipped away by Danilo Emanuel.
N'Doye could have put Senegal in front five minutes after the restart, but he could only see his header fly wide.
Equatorial Guinea made the breakthrough on the hour when Iban Travieso headed in Kily Alvarez's cross.
After further chances for Papiss Cisse and Mamadou Niang, Senegal grabbed an equaliser with a minute to play when Moussa Sow hit home following a scramble in the penalty area.
However, there was time for late drama as Kily smashed in from 20 yards to seal the win.
Despite the wild scenes, Equatorial Guinea's win was tempered by Laurence Doe's sending off in the final seconds after he picked up a second yellow card for time wasting.