Dieumerci Mbokani and Jordan Nkololo scored for the Leopards, as they beat the former African champions, who were below par in the match.
The unimpressive Eagles were first punished as early as the sixth minute after Yannick Bolasie crossed for Mbokani to fire past Carl Ikeme. Nkololo doubled their lead in the 41st minute of play.
The Eagles through returnee midfielder Mikel Obi and Ogenyi Onazi made some faint attempts to restore parity but their effort did not provide required result.
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Nigeria will take on Cameroon on Sunday.