The win gave the Taifa Stars a 2-1 aggregate victory after they lost 1-0 to the Harambee Stars a fortnight ago in Nairobi.
The match was not helped by torrential rain that made the astro-turf pitch almost unplayable, but Kenya goalkeeper Joseph Ruto will feel he could have done better for both goals.
Jerry Tegete's strike at the near right post went under Ruto's diving body, while he also made a mess of punching a corner-kick clear in the 93rd minute, with Naddin Haroub scoring from the loose ball.
The next round of matches take place on the weekends of May 2-4 and May 16-18, with Tanzania at home in the first leg.