The CSKA Moscow forward latched on to a visionary ball from Efe Ambrose and had the composure to loop high and over the committed Duncan Ochieng.
Nigeria went into the game top of the group but walking a tightrope after opening the door and allowing Kenya a peek in the reveres fixture last March.
But the Harambee Stars were hamstrung by the loss of four key players, and were underdogs despite playing at home.
However, with Victor Wanyama a controlling figure in midfield, they frustrated Nigeria and made life hard for John Mikel Obi's midfield.
Both chances created chances, even though Nigeria dominated most of the possession.
Wanyama however, picked up a knock in the second half, and his influence apwaned, Mikel's grew, with the Nigerian dictating play and looking to jack up the game.
Kenya's strategy though, proved to be their undoing. Waruru broke free on the counter and bore down menacingly down the left channel.
With no support, he tried to take on Efe Ambrose. The Celtic man calmly dispossessed him, then raked a long, looping punt to Musa, whose pace got him in behind the Stars defence.
Ochieng, way off his line, was caught unprepared. Nonetheless, Musa had the not so easy task of hooking the ball way high of Ochieng and into the net.
It proved to be the decider, but just to make sure, Stephen Keshi threw on Fegor Ogude to steady the ship as Nigeria held on for the win.
With second placed Malawi drawing with Namibia, the Super Eagles establish daylight at the top of the group.
Victory over Namibia next week will see the Super Eagles needing just a draw against Malawi at home in their final group game if the Flames win against Kenya.
If Malawi fail to beat Kenya, the Super Eagles will qualify with one game to spare.