Birwa Nouri put the home side ahead in the 16th minute, from the spot after Samuel Onyango fouled him in the penalty area. Harambee stars chased shadows for the better part of the match with Ahmed Khalaf adding the second just after the restart.
Girona striker Michael Olunga who missed two clear chances pulled one back in the 85th minute. Coach Stanley Okumbi’s charges play Thailand On Sunday in another friendly match.
Elsewhere, Harry Kane's injury time winner secured England's qualification for next summer's World Cup, with a victory over Slovenia.
Meanwhile, Scotland kept their qualifying hopes alive in dramatic fashion as a late Martin Skrtel own goal gave them a 1-0 win against 10-man Slovakia, while defending champions Germany confirmed their qualification by beating Northern Ireland 3-1 in Belfast.
Other results saw Denmark beat Montenegro 1-0, Czech Republic were 1-0 winners over Azerbaijan, Norway thrashed San Marino 8-0, while Poland hammered Armenia 6-1.