Boye saw red for a second bookable offense. He left a free-kick for goalkeeper Richard Ofori to take and the centre referee who suspected him of mapping up delaying tactics flashed the yellow card at him in what was his second bookable offense in the game.
John Boye was shown a yellow card in the first half for fouling his opponent.
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In the game Mickael Pote fired Benin into the lead under two minutes, which is the fastest goal thus far in the competition.
But Andre Ayew snatched the equaliser for the Black Stars seven minutes afterwards.
Before Jordan Ayew put Ghana in the driving seat a few minutes to the half time break.
The tide changed after the break when John Boye was handed a second booking for delaying tactics and Benin capitalised on that to secure the equaliser.
Pote put the Squirrels on level pegging when he scored from a nice backheel in the 77th minute.
The match ended, Ghana 2-2 Benin.