The Flames were looking to depose leaders Nigeria, who play Namibia in Windhoek tonight, and Robin Ngalande’s opener in the 46th minute put them on the right track.
Jamal Mohammed equalised for Kenya six minutes later but the hosts thought they had the winner when Robert Ng’ambi found the back of the net nine minutes from full-time.
Kayira, though, put through his own net with one minute remaining, leaving Malawi a point shy of top spot while Kenya remain bottom with just three points from five games.
A Nigerian victory in Namibia would leave Malawi unable to progress to the third round of qualifying with only one round of games remaining.
GROUP F STANDINGS
Nigeria – 8 points
Malawi – 7 points
Namibia – 4 points
Kenya – 3 points