Stars unbeaten run ends as they start Nations Cup campaign on poor footing.
Harambee Stars started their 2019 Africa Cup of Nations qualifier on a sour note after going down 2-1 to Sierra Leone on Saturday.
Kei Camara put the hosts ahead in the 22nd minute before Umaru Bungara added a second in the 70th minute from the spot.
Michael Olunga's 76th minute goal was not enough to ensure at least a point for Stars.
Stars were forced to play a man less from the 43rd minute after Brian Mandela was sent off for a professional foul.
In the first half, Harambee Stars only picked up from the quarter hour mark creating several chances which they failed to utilise.
Meanwhile, Vincent Aboubacar's goal gave Cameroon a 1-0 win over Morocco in their 2019 CAF Africa Cup of Nations Group B qualifier on Saturday at Stade Omnisport Ahmadou Ahidjo in Yaoundé.
The hosts came into this encounter backed by their vocal supporters at home and were the favourites to claim the full three points.
As soon as they made their way onto the pitch, Hugo Broos's men showed hunger as they dominated the proceedings over their visitors.
Although the first 20 minutes had no goals for either side, it was the African champions who wanted it more as the Atlas Lions were yet to threaten.
However, as the tie approached the half-hour mark, Aboubacar received a wonderful pass from the midfield and he managed to beat two Moroccan defenders, before putting the ball past the onrushing goalkeeper, Munir El Kajoui.
It was 1-0 at halftime.
Upon their return from the tunnel, the hosts enjoyed the majority of the ball possession, yet failed to double their lead as Herve Renard's defence stood firm.
Although they will automatically qualify to reach the 2019 CAF Afcon tournament, the Indomitable Lions are now sitting at No 1 with three points.
They are the group's joint leaders with Malawi on three points and one goal, who beat Comoros on the same day.
For the Atlas Lions, the loss means they remain rooted at the bottom of the log table with zero points from one match.