Emenike marked his return to action for the national team with a goal in the 45th minute, to give a dominant Nigerian team a well-deserved lead over Malawi.
Before the goal, Nigeria dominated proceedings and made several incursions into the vital area of the Malawians, but the Southern African nation were comfortable sitting back to soak the pressure, as they launched a few futile counter attacks from the flanks.
The Flames however had a rare chance at goal in the 39th minute when Azubuike Egwuekwe mistimed his run and allowed Charles Swini to cut in from the left and send in a cross that was saved by a last ditch header from Efe Ambrose.
The second half resumed in explosive fashion, with Musa getting a free chance at goal in the 47th minute. The CSKA Moscow forward however miscued his pass to Emenike, allowing the Malawians to deal with the threat.
A minute later, Emenike missed a sitter after being played on goal by Ahmed Musa.
Nigeria would however get the much yearned second goal, as they were awarded a penalty after a goal bound Nnamdi Oduamadi was brought down in the 50th minute.
Victor Moses stepped up a d concerted the resulting penalty to double Nigeria's advantage, and put the Super Eagles on cruise control, as they dominated the game from that moment.
The Malawians suffered a blow shortly after, as Limbikani Mzava was given the marching orders for a second bookable offence.
With the points already secure, Nigeria's coach Stephen Keshi took off Moses for Nosa Igiebor in the 71st minute as Nigeria continued to threaten and were unlucky not to increase their lead, with the Flames of Malawi managing to avoid a rout.
In the latter stages of the game, Emenike and Oduamadi made way for Shola Ameobi and Uche Nwofor respectively.