Sunday Mba's volleyed goal five minutes before half-time ended the fairytale run of the Burkinabe, who had exceeded all expectation by advancing to their first final.
Nigeria proved too strong in the deciding match for the workman-like Burkinabe, who were out-muscled and out-sprinted at Soccer City and never looked like repeating the heroics that got them to the final.
Mba's goal came from a botched clearance that fell perfectly for him but he conjured up a piece of brilliance by flicking the ball over the head of defender Bakary Kone and then slamming it into the net with goalkeeper Daouda Diakite rooted to his line.
It was one of just a few clear chances on the night, most of them for Nigeria who looked a class above their game but outgunned opponents.
Nigeria, whose coach Stephen Keshi became the second man to win the Nations Cup as both coach and player, might well have added two or three more too the score with a little extra care in front of goal.
Brown Ideye had chances just after halftime and again with eight minutes to go but overran the ball and Ahmed Musa slipped at a crucial moment when he was put in the clear by Victor Moses.
Moses was also guilty of squandering opportunities on the counter attack as Burkina Faso were kept pegged back in their own half.
John Obi Mikel in midfield ensured Nigeria had a tight grip on the game, but there were half-chances for the Burkinabe and one moment when they might have equalised when Wilfried Sanou shot a snap effort just across the face of goal in the 73rd minute.
Burkina made a gallant effort near the end to try and snatch an equaliser, as they had when the two teams met in the group phase at the start of the tournament.
"You don't want to know what was going through my mind in the closing minutes," said Keshi, whose team cleverly closed out the game.
"Perhaps we were tired but I don't want to make excuses," said Burkina Faso's coach Paul Put told reporters. "I saw my team fighting to the last minute, I'm very proud, all Burkinabe can be proud of these players."
The Nations Cup victory was Nigeria's third, following on previous success in 1980 and in 1994, when Keshi was captain.
They now play in the Confederation Cup in Brazil where they will face Oceania champions Tahiti, South American champions Uruguay and world champions Spain.
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