DR Congo thought they had taken the lead after four minutes by referee Jelly Chavani ruled out Jephte Kitambala's goal after consulting VAR for a possible foul.
With Congo, the more threatening side, they struggled to turn that into goals and were punished when Austine Odhiambo beat the halftime whistle to put Kenya.
After being set up, he shrugged off the challenge of Leopards' defenders to superbly finish and thrust the hosts ahead in the first half's stoppage time.
Odhiambo's goal was the decider and the match ended 1-0 in favour of the Harambee Stars, who are coached by Bafana Bafana legend Benni McCarthy.