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Asamoah Gyan drew first blood in the clash by putting Niger on the backfoot in the sixth minute with a powerful shot into the back of the net.
The former Sunderland striker found the ball in acres of space and a vital first touch allowed the frontman to set up his shot and blast it into the back of the net.
Niger instantly responded through Moussa Maazou, who equalised for his nation, but it was swiftly ruled out after he was penalised for fouling the goalkeeper while he was driving towards goal.
Niger had time to build again but their hopes were dashed when Christian Atsu slotted the ball home from Gyan, who picked out his teammate in the box with a cross, which bypassed Niger's defence.
Ghana went from strength to strength in the second half by taking a three-goal lead courtesy of a header from John Boye, who took his chance when the ball rebounded off the goalkeeper from Gyan's initial headed attempt.
The uphill struggle was too much for Niger to come back from and they relinquished a place in the final eight of the competition.