Julius Wobay scored in the first half and skipper Umaru Bangura added a second from the spot with Michael Olunga scoring Kenya’s late consolation later.
For the missed opportunity, Kenya was punished four minutes on the turn. Wobay met a cut back from a Kei Kamara cross on the left and he shot first time, and despite Boniface Oluoch having a touch on the ball, it hit the inside of the upright before rolling into the net.
Kenya captain Victor Wanyama came close to making an immediate response but his header hit the crossbar after racing to meet a free-kick from Eric Johannah.
The visiting Harambee Stars continued creating chances but failed to utilize them. In the 34th minute, Johannah had a chance from a free-kick but he sent it straight to the keeper.
Two minutes later, double open scoring chances again went begging. Wanyama’s shot from a Johannah pass was blocked by Morris and Olunga struck the crossbar with a rebound.
Five minutes to the break, bad was to turn to worse for Kenya with defender Brian Mandela being sent off for a rush tackle on Alhassan Kamara as the last man in defense.
In the second half, Harambee Stars head coach Stanley Okumbi made a change necessitated by the red card, bringing on David Ochieng for Massoud.
The Leone Stars found a way to maintain the tempo and in the 56th minute, Alhassan came close to adding a second but he slipped as he pulled the trigger when he met a cross from the right.
On 70 minutes, they homers went 2-0 up from the spot after Kenya left back Erick Marcello axed Kamara inside the box, and Bangura stepped up to convert home.
Olunga gave Kenya some hope in the 75th minute when he wonderfully curled home a freekick from the edge of the box for what turned out to be the consolation.
Ghana host Ethiopia in the other Group F match later on Sunday in Kumasi.
9.06.2017 Obeid Sudan 1-3 Madagascar
10.06.2017 Dakar Senegal vs Equatorial Guinea
10.06.2017 Yaounde Cameroon 1-0 Morocco
10.06.2017 Lilongwe Malawi 1-0 Comoros
10.06.2017 Bamako Mali 2-1 Gabon
10.06.2017 Bujumbura Burundi 3-1 South Sudan
11.06.2017 Blida Algeria vs Togo
11.06.2017 Cotonou Benin vs Gambia
9.06.2017 Cairo Libya 5-1 Seychelles
10.06.2017 Uyo Nigeria 0-2 South Africa
10.06.2017 Freetown Sierra Leone 2-1 Kenya
11.06.2017 Kumasi Ghana vs Ethiopia
10.06.2017 Kinshasa DR Congo 3-1 Congo
11.06.2017 Harare Zimbabwe vs Liberia
10.06.2017 Bouake Cote d’Ivoire 2-3 Guinea
11.06.2017 Bangui Central African Rep. vs Rwanda
10.06.2017 Ouagadougou Burkina Faso 3-1 Angola
10.06.2017 Francistown Botswana 0-1 Mauritania
10.06.2017 Niamey Niger 0-0 Swaziland
11.06.2017 Tunis Tunisia vs Egypt
10.06.2017 Ndola Zambia 0-1 Mozambique
10.06.2017 Bissau Guinea Bissau 1-0 Namibia
10.06.2017 Dar es Salaam Tanzania 1-1 Lesotho
11.06.2017 Praia Cape Verde vs Uganda