Stars captain Michael Olunga and midfielder Richard Odada scored in the first half as Kenya registered their first win in the qualifiers. Oliver Niyonzima scored Rwanda's consolation goal in the second half.
Kenya headed into the match behind their 1-1 draw against Uganda Cranes last week on Thursday, the same day Rwanda lost 1-0 to leaders Mali.
With both teams having being lost the chance to advance into the last phase of the qualifiers, they were playing just for pride.
And after 90 minutes, it was Kenya who had the last laugh and putting a smile on the face of Turkish coach Engin Firat, who is expected to leave his role with the expiry of his two-month contract.
