Badou Ezzaki's Morocco wrapped up a two-game swing in winning fashion, with El Mehdi Karnass, Mbark Boussoufa and Mouhcine Iajour all scoring in the final 15 minutes.
Kenya bravely held out for 76 minutes at the Stade de Marrakech, before Karnass - in just his second international appearance - struck the opener for the hosts.
The defensive aspect of Adel Amrouche's men had been their focus but their goal was peppered in the dying stages - as Boussoufa converted from the spot four minutes from time, for his sixth goal for his country.
Iajour added a third in the 89th minute, as Morocco celebrated their third win in a row, and second in four days after a 4-0 win over Central African Republic.
It was Iajour's fifth goal in his ninth cap.
Kenya are without a win in six internationals, losing three of their past four.
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