Harambee Stars went into the away game seeking victory but forward Serhou Guirassy had other ideas as he scored what turned out to be the winner for Guinea in the 32nd minute.
Kenya coach Benni McCarthy made two changes to the squad which faced Eritrea in the 1-1 draw, with midfielder Mohamed Bajaber starting alongside Ben-Stanley Omondi.
The game started with Guinea winning a free-kick from outside the area, but the resultant effort from Oud-Heverlee Leuven forward Abdoul Karim Traore hit the Harambee Stars wall.
In the 10th minute, Kenya started to settle, and it was Micah Obiero who had the first opportunity to score for the East African side after breaking through Guinea's rearguard but his effort was saved by Mohamed Camara.
Guinea the better side
Four minutes later, Guinea threatened again, this time dangerman Serhou Guirassy watching helplessly after his superb free-kick rattled the upright side of the post for a goal-kick.
Kenya continued to lose the ball and give away free-kicks in their own half, with Bajaber becoming the first player to go into the referee’s book. Guirassy teed up Karim Traore with a fantastic pass but the latter hit his effort wide.
Guinea looked the most likely side to break the deadlock, and they did so in the 32nd minute. Borussia Dortmund talisman Guirassy picked the ball from the area, surged forward while dribbling past Kenyan defenders and snuck it past Bryne Omondi.
The goal for Guinea was coming, as they had missed a couple of chances, including a glancing header by Yadaly Diaby, before Guirassy calmly picked the right corner for the opener.
Guinea continued to attack Kenya for the second, but Omondi did well to deny Abdulkarim Traore and Guirassy before the whistle for the half-time break saved them from a disastrous result.
Ogam misses chance for Kenya
At the start of the second period, McCarthy looked to the bench and summoned youngster Ryan Ogam, who scored against Eritrea, to replace Job Ochieng, while Obiero was rested for Timothy Ouma.
Guinea coach Paulo Duarte made one change which saw Mory Konate come in to replace Aboubacar Keita at the back.
Ogam almost scored for Kenya in the 55th minute after he created space inside Guinea’s danger zone, but Camara pulled off a superb save to deny the former Tusker FC man.
Bajaber was the third player for Kenya to come off as Sharif Musa was introduced in the 60th minute while Guinea rested Seydouba Cisse for Ibrahima Sory Bangoura. Javan Omondi was handed his debut for Kenya, replacing Stanley Omondi.
Following the defeat, Guinea moved above Kenya to second spot in Group D with three points, while South Africa remained top with a maximum six points following their 5-0 victory against Eritrea.
Kenya have already qualified automatically as co-hosts, and only the highest-placed side among South Africa, Guinea and Eritrea will join Kenya at PAMOJA 2027 AFCON in East Africa.
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