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The Super Eagles were the dominant force during the first half and went into the break with a healthy advantage thanks to three unanswered goals.
Having missed a couple of chances during the opening exchanges, the Nigerians broke the deadlock with 25 minutes played. Chelsea's Victor Moses worked himself some space out on the right wing to send over a cross for Elderson Echiejile, who stooped to head the ball into the net.
Spartak Moscow's Emenike played a major role in his nation's third goal one minute before the break when his free kick deflected into the net off former Liverpool midfielder Mohamed Sissoko.
Despite their winning margin, Nigeria continued to attack after the restart and Mali goalkeeper Mamadou Samassa was beaten for a fourth time on the hour mark. Just moments after he had replaced Moses, Musa Ahmed broke the offside trap to score with a low effort.
The same player thought he had scored again two minutes later, but his goal was ruled out for offside.
As Nigeria looked to protect what they had, Mali were able to claim a consolation in the 75th minute when Cheick Diarra capitalised on hesitation in the defence to drill the ball in from 15 yards out.
Nigeria will now take on either Burkina Faso or Ghana in Sunday's final.