Namibia, with an overnight lead of 207, held the upperhand into the final day but the hosts fought back to bridge the gap thanks to an unbeaten 187 by opener Ravindu Shah.
Kenya were 43 runs short of levelling the series when the Namibian captain Deon Kotze decided they had had enough and surrendered the victory to his opponents.
The draw put Kenya on top of the three-nation qualifying tournament which also involved Uganda.
They finished with 45.5 points, with the Ugandans, who beat Namibia by five wickets in Windhoek, in second place with 41 points, while Namibia finished third on 33 points.
The Kenyans will now play Scotland in the ICC continental Cup semi-finals in Sharjah in the United Arab Erirates in November.