Musa latched onto a through ball from John Obi Mikel to beat his marker David ‘Cheche’ Ochieng’ before beautiful chipping the ball over the advancing goalkeeper Duncan Ochieng’ in Kenyan goal.
The win now takes Nigeria back to the top of Group F with 8 points while Malawi are second on six after battling to a 0-0 draw with Namibia in a match played in Blantyre earlier on Wednesday.
Kenya, who had win to keep alive their hopes of gracing the World Cup final, started the match badly with defender Brian Mandela almost handing the visitors a quick goal in the 1st minute of the match.
The South African-based defender failed to deal with a loose ball after restart allowing Nigerian striker Brian Ideye to charge forward but the Super Eagles' star could not find the back of the net with keeper Ochieng’ to beat.
Five minutes later, Musa Ahmed beat the Kenyan defense but his attempt to pick out an advancing Sunday Mba was blocked by Brian Mandela.
The Kenyans were having a great time in midfield and Oman-based Jamal Mohammed was showing some awesome creativity though he appeared self-fish sometimes.
In the 10th minute with Kepha Aswani advancing towards the Nigerian goal, Mohammed hesitated and allowed the Nigerian defense to recover lost ground.
One minute later, Nigeria had their first free-kick which Chelsea star John Obi Mikel lifting it high towards the Kenyan goal and rested on the side netting.
Duncun Ochieng in goal threw the ball quickly to a running Victor Wanyama but he failed to keep it into play. In the 13th minute, the visitors got their second free-kick just near the Kenyan goal but Musa Ahmed's shot was defended well.
Kenya got the first corner in the 24th minute when Francis Kahata efforts to beat Efe Ambrose in the Nigerian defense ended in vain.
Ambrose was forced to come out and stop Kahata once again in the 29th minute after Jamal Mohammed had picked him out with a splitting pass but Stars could only get a corner from the effort.
Kepha Aswani making his return to the Kenyan team after a long time was a pale shadow of himself and he looked injured as he time and again limped. He never made any effort at goal allowing Vincent Enyeama to have a long rest in the first half.
Nigeria got their first corner of the match in the 34th minute when a goal bound Musa Ahmed was stopped in his tracks by David Ochieng.
Four minutes later, Ahmed's shot was deflected by Mandela and calmly picked by Duncun Ochieng’, who made a throw to Johanna Omollo and he made the first attempt at goal but his effort was stopped by Vincent Enyeama.
The Kenyans were gaining confidence as the first half wore off and Peter Opiyo made the second shot at the Nigerian goal in the 39th minute.
Nigeria got their second corner in the 43rd minute but it was the home team who ended the first half on a high note with Victor Wanyama coming close only to shoot wide.
The worst would come with less that 15 minutes left to play, Stephen Waruru giving away possession cheaply in the opponent’s third, a counter attack resulting in Ahmed Musa lifting the ball over an advancing Duncun Ochieng.