The two sides, who reached the second round of qualifying with two-legged wins over Seychelles and Djibouti respectively, entered the fixture in Nairobi with no chance of making the third round.
They both struggled in Group F, with Adel Amrouche's side were winless in their five group matches, while Nairobi's only win was a 1-0 triumph against Kenya last year.
Pride was all that was on the line at the Moi International Sports Centre and it was Kenya who won it, thanks to an early goal.
David Owino was the scorer, with the defender firing Kenya into a fifth-minute lead.
Namibia pressed valiantly for an equaliser but Kenya, led by Southampton star Victor Wanyama, held on for all three points.
As a result of their victory, Kenya moved above Namibia and to third in the Group F table.
The qualifying campaign for both nations is over now, with Nigeria progressing, as expected, to the third round after topping Group F.
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