Ahmed Musa notched the winner nine minutes from time racing onto a long ball before coolly lobbing goalkeeper Duncan Ochieng to give the Super Eagles a deserved victory at Moi International Sports Centre Kasarani.
It capped off a brilliant afternoon for Musa who tormented the Kenyan backline throughout the match with pace and trickery.
Nigeria now has eight points from four games, two ahead of Malawi who were held to a 0-0 draw by Namibia in Blantyre. For Stars, their hopes of a place in Brazil next are almost over as they prop up the group on two points.
Missing skipper Dennis Oliech and Arnold Origi, Stars started shakily and they almost gifted Nigeria the lead on five minutes after a mix up between Ochieng and Brian Mandela presented Brown Ideye with a chance but he blazed over.
Musa then went close with a freekick on 14 minutes after Ideye had been fouled as Stars struggled to get a foothold in the match.
Kenya’s first sight goal came on the half hour mark but Mandela headed Francis Kahata’s corner wide. Vincent Enyeama was a bystander for most of the half waiting till the 39th minute to make his first save of the match gobbling up Peter Opiyo’s long range effort.
Stand in skipper Victor Wanyama had been Stars’ best player in the opening half but he was unable to keep his shot down after neat interplay between Kahata and Jamal Mohammed on the stroke of halftime.
Nigeria should have gone ahead in the opening minute of the second half when Nnamdi Oduamadi skinned Mandela in the box but Ochieng was quick off his line to make a fantastic save with his feet to keep the scores level.
An injury sustained by Wanyama slowed down the hoists as he was unable to patrol the middle of the park with the same effectiveness a she had in the first half.
The introduction of Anthony Ujah gave them more impetus as they pushed Kenya deeper and deeper with the giant Nigerian providing physical presence in the box.
He headed a cross just wide on 72 and four minutes later, Obi Mikel fired just over from range.
The goal finally arrived on 81 minutes and it was one of stunning simplicity.
Substitute Stephen Waruru lost the ball on the edge of the Nigerian box and from the resulting long ball, Musa held off Mandela and Ochieng before chipping the goalkeeper and quieten the partisan crowd in the stadium.
Nigeria next face Namibia in Windhoek while Kenya travel to Blantyre for a date against the Flames of Malawi.