Johanna Ochieng Omolo's strike in the first leg ensured Kenya took a 1-0 lead into Friday's second leg at the Stade International Said Mohamed Cheikh de Mitsamiouli.
Adel Amrouche's charges faced early pressure as the hosts sought to level the tie, but Comoros were unable to turn their dominance into goals.
The hosts were punished in the 56th minute when Ayub Timbe Masika opened the scoring with an expertly taken free-kick that left the goalkeeper with no chance.
Poor defending from Kenya allowed Yacine Saandi to level the scores on the night with 18 minutes remaining.
However, his goal proved in vain as Kenya prevented Comoros from levelling the tie on aggregate.
Mozambique were held to a 0-0 draw by South Sudan in Friday's other fixture, but were already virtually certain to progress after a 5-0 first-leg win.
