Burly striker Vincent Oburu scored the decisive goal in the 20th minute that proved vital for the home side after close rivals Libya enyoyed a shock 1-0 win over the group pacesetters, Zanzibar in the early kick-off at the Kenyatta stadium in Machakos.
The result put Kenya at the top of the five-team group on eight points ahead of Zanzibar, who have seven points while Libya, only taking part as guests finished an impressive third on six points.
Kenya will now meet Burundi in the first semi-final on December 14 in Kisumu, with Zanzibar taking on holders, Uganda the following day.
Burundi finished second in Group B after being held to a scoreless draw by lowly South Sudan in the final group match in Kakamega on Monday.
The draw for the Bright Stars means they could only manage to pick one point from the three group matches, having conceded eight goals, to finish at the bottom.