The home side came into the match knowing that anything other than a defeat would see them advance to the final stage of African qualification, with Malawi needing three points if they were to keep their slim hopes alive.
Victory for the African champions never looked in doubt as they showcased some entertaining football and claimed maximum points thanks to a well-worked goal from Emmanuel Emenike and a penalty from Victor Moses, as Malawi finished the game with 10 men.
Nigeria coach Stephen Keshi named three changes from the team's last qualifier against Namibia in June as Emenike, Moses and Azubuike Egwuekwe came in for Kenneth Omeruo, Sunday Mba and Anthony Ujah.
Second-placed Malawi also last played a qualifier in June as they were held to a 2-2 draw at home to Kenya thanks to Moses Chavula's own goal, but the 28-year-old was one of six players to keep his place in the team, with manager Tom Saintfiet making five changes.
The hosts took control of the match early on and spent most of their time in the attacking third, but for all their encouraging play they struggled to get shots on target as Ahmed Musa fired over from close range after Malawi failed to clear a corner.
Malawi showed attacking initiative when trying to catch Nigeria on the counter-attack, but Keshi’s defenders proved to be up to the challenge, while right-back Efe Ambrose almost broke the deadlock as he headed wide after beating goalkeeper Charles Swini to Moses' corner.
Ambrose was proving to be a threat and he had an opportunity in the final 10 minutes of the first half as he skipped past a defender down the right before firing at goal, forcing Swini into a good save.
Malawi looked as though they would be heading into the break level, but Emenike had other plans as he darted into the area, controlled Ogenyi Onazi's fantastic lofted pass from deep and lifted the ball over the approaching Swini for a half-time lead.
Nigeria began the second half at a ferocious speed and after early chances for Musa and Emenike, they extended their lead from the penalty spot. Nnamdi Oduamadi won the decision after linking up with Musa, and Moses calmly stroked home from the spot.
The visitors' nightmare start to the second half got even worse in the 53rd minute as Limbikani Mzava callously hacked Musa down just outside the area, picking up his second yellow card after earning a cheap booking at the beginning of the match.
Emenike should have doubled his tally with 15 minutes remaining, but after excellent work by Musa on the left wing the Fenerbahce man somehow managed to divert the ball over the goal from a few yards out.
