Sunday Mba's goal in the 40th minute delivered another triumph for coach Stephen Keshi after he captained Nigeria to its last African Cup crown in 1994.
Mba decided the game in front of around 87,000 fans at Soccer City with a left-foot volley into the far right corner after he expertly controlled a rebound and clipped the ball over a defender.
Burkina Faso fell short of what would have been a surprising triumph in its first final, having progressed beyond the group stage for only the second time at the African championship.
Mba's goal came after Victor Moses' shot was blocked, and was worthy of deciding a final. In three swift motions, Mba controlled the ball, chipped it over Mohamed Koffi and then volleyed across goalkeeper Daouda Diakite and into the far right corner.
It was enough to give Nigeria its third African Cup title and make Keshi just the second man to win the tournament as both a player and coach.
Wilfried Sanou sent a powerful low shot just wide in the 74th minute for Burkina Faso but Nigeria controlled most of the game and wasted several good chances to extend its lead.
The victory also made Nigeria the last country to qualify for June's Confederations Cup in Brazil as continental champion.
Keshi brought Joseph Yobo off the bench in the 89th minute to give the veteran defender and regular captain a chance to finally lift the trophy in his sixth African Cup.
Nigeria's Efe Ambrose hit the first shot of the game inside a minute and then headed a free kick from Moses just over the crossbar in the seventh.
Moses also caused trouble for the Burkina Faso defense and Nigeria was far more enterprising than its underdog opponent in the first quarter.
The Chelsea forward beat his marker down the left wing in the 20th — having also threatened earlier down the right — and put in a dangerous low cross that Diakite smothered.
Tall blonde-haired striker Aristide Bance had Burkina Faso's first real effort in the 25th, but sent it rising high and to the right of Vincent Enyeama's goal.
Bance's 28th-minute free kick then skipped just wide of the left post as the Burkinabes began to slowly find their feet in their country's biggest ever game.
The teams retreated to cautious play toward the end of the first half, with the sellout crowd at Soccer City responding with a wave around the stadium.
Bakary Kone's header at the back post from Charles Kabore's deep free kick seven minutes before halftime was well wide.
Minutes later, Mba's strike gave the Nigerians a deserved lead as his surging run, juggle and quick-witted volley left Diakite stationary near his goal-line as the ball flew past him.
Brown Ideye hit a low shot across the Burkina Faso goal in the opening minutes of the second half after more work from Moses as Nigeria remained in control.
Burkina Faso was looking to cause a similar upset to Zambia's victory a year ago, but found its first major final tough going at Johannesburg's 2010 World Cup final venue, having played all their previous games in Nelspruit. Star player Jonathan Pitroipa, who was cleared to play after having a red card from the semifinals rescinded, failed to make an impact in the game.
Nigeria seemed content with defending its slender lead from around the 70th minute and Burkina Faso began to make some late progress.
After Musa Ahmed slipped when through on goal for Nigeria on a counterattack, Sanou sent his blistering low shot from the right inches past the left post for Burkina Faso in one of their best chances for an equalizer.
Nigeria then twice went close in the 86th, but couldn't find the sharp finishing to double the lead.
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