Michael Pote gave Benin a shock second-minute lead in the Group F match before goals from brothers Andre and Jordan Ayew put Ghana 2-1 ahead at halftime of an entertaining, end-to-end contest.
But Ghana were stunned in the 55th minute when defender John Boye, already booked, stepped up to take a free kick inside his own half, moved away to let goalkeeper Richard Ofori take it and was given a second yellow card.
It seemed no more than a misunderstanding, was extremely harsh and was also the first sending-off of the tournament.
Pote then equalised for Benin with his second of the night in the 64th minute.
Benin, taking part in the tournament for the fourth time, had lost eight and drawn one of their nine previous games at the finals but more than held their own against the four-times champions.
The Squirrels were in front after two minutes, Pote racing onto a ball threaded through from midfield before slipping past his marker and firing his shot under Ofori.
Ghana replied with a goal from their first attack seven minutes later. Jordan Ayew ran onto a pass over the top and laid the ball off to his brother Andre who made space before firing a snapshot into the net.
Ghana, looking more dangerous, went ahead three minutes before halftime. Kasim Adams picked out Jordan Ayew from the halfway line and the younger of the two brothers slipped passed Olivier Verdon and fired into the top corner from the edge of the penalty area.
At that point, the game seemed to be up for Benin but Boye's dismissal changed the complexion of the game, prompting Ghana coach Kwesi Appiah to bring off Samuel Owusu -- himself a first-half substitute for the injured Thomas Agyepong -- and bring on Jonathan Mensah.
Benin's equaliser came from a short corner as Pote diverted Cebio Soukou's low cross into the net.
Both teams continued to look for the winner and Thomas Partey was close for Ghana with a ferocious 25-metre free kick which Fabien Farnolle did well to push away.
Benin could also have snatched it in injury time as Jodel Dossou's cross from the right picked out Steve Mounie but he sent his header over the bar.
Following the opening round of games, Cameroon top the group with three points following their 2-0 win over Guinea Bissau earlier on Tuesday.
(Writing by Brian Homewood; Editing by Toby Davis)
