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Harambee Stars secured opened the scoring thanks to a sensational free-kick from John Avire in the 57th minute.
The Brave Warriors dominated the game in the first half, creating many opportunities, but Kenya's defence was resolute.
In the second half, the Southern Africa side started well and came close to scoring, but the ball couldn't go in.
In the 59th minute, the East Africans won a free kick a few yards from the box and up stepped Avire, who fired a superb shot past Lloyd Junior Kazapua.
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Duke Abuya added a second in the 77th minute following a sensational counter-attack. Engin Firat's side survived dangerous attacks from the Brave Warriors, especially in the first half.
Unlike the Zimbabwe game, Kenya decided to sit back and cede control of the ball, a decision which almost cost them. Deon Hotto scored Namibia's consolation goal in the 95th minute.
Kenya are now top of Group J with four points, level with Cameroon, who drew with Zimbabwe in their other match.
Kenya is chasing only their third AFCON spot in 30 years, and four points from their two games is a positive start, per Nation Sports. They face giants Cameroon in back-to-back matches in October.
TUKO.co.ke earlier reported that Jacob 'Ghost' Mulee discussed Kenya's chances of reaching the Africa Cup of Nations in 2025, which will be hosted by Morocco.
The former Harambee Stars coach, who led the team at the 2004 tournament, believes they have good squad players who can help them qualify.
TUKO.co.ke also reported that Harambee Stars coach Engin Firat expressed his thoughts about Kenya's football infrastructure.
The Turk was in awe of Uganda's stadium which his team played on, saying Kenya can only "dream about them."
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