Remo Stars beat visiting Katsina United 2-1 to finish as runners-up on 65 points, five points adrift of champions Enugu Rangers.
They will play in the CAF Champions League along with Rangers.
Last season champions Enyimba stopped Plateau United 2-0 at home to finish third on 63 points.
They will feature in the second-tier CAF Confederation Cup.
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