The Super Eagles were helped by goals from returnee striker Emmanuel Emenika and a penalty from attacker Victor Moses.
The game began on a very competitive note with Liverpool loan signing Moses and Ahmed Musa tormenting the James Sangala-anchored Malawian defence. As early as the second minute, Limbikani Mzava was booked for a rough challenge on Moses who was on a goal-bound move.
Despite gaining most of the ball possession, Nigeria failed to get the curtain raiser as they failed to create clear cut chances. The attack-minded Eagles did not relent as they challenged Tom Santifiet’s men for every ball.
In the 11th minute, Musa saw his opportunity declared offside after he got a well-tailored cross from John Obi Mikel. Few minutes later, Ogenyi Onazi's shot went just wide as Stephen Keshi's men continued their search of the early goal.
Malawi shot-stopper, Simplex Nthara repaid the faith shown in him by Tom Saintfiet to start the game with a brilliant save off the boot of Efe Ambrose followed by another super effort in the 26th minute to deny Moses the opening goal.
As the first half petered out, Emenike put Nigeria ahead with a very cool finish off a pinpoint cross from Onazi. Despite resolute defending from the Malawians, they allowed the Fenerbahce striker sneak in to chip the ball past Simplex to calm the nerves of the hosts.
In the early minutes of the second half, Musa failed to double Nigeria’s lead after missing a one-on-one opportunity with the goalkeeper who gathered safely to keep the Flames in the game. Shortly afterwards Emenike was denied by the same goalkeeper.
The Eagles, however, put the game beyond the reach of the Malawians in the 51st minute after Brescia forward Nnamdi Oduamadi was forcefully brought down by Flames skipper James Sangala. Moses shot the resultant penalty past Simplex to give the Eagles a comfortable lead.
A few minutes later, the visitors were reduced to 10 men after Limbikani Mzava was sent off for a second yellow to compound Malawi's misery.
Musa's battle with the Malawi goalkeeper continued in the 68th minute as he was unable to score again in a one on one situation. Even with the introduction of Newcastle forward Shola Ameobi for his competitive debut, Nosa Igiebor and Uche Nwofor, Nigeria failed to get the third goal after missing several scoring chances.
With this result, Nigeria are now through to the final play-off round of World Cup 2014 qualification and will know their opponents when the draw is made in a few days.