Forward Mirikat Feleke opened the scoring for the hosts in the 19th minute and ten minutes later, they went two-up courtesy of an Alemnesh Geremew strike for a 2-0 lead at halftime in the match played at the Hawassa Stadium.
The junior Starlets rallied back after the break and pulled a goal back through skipper Corazon Aquino 's penalty in the 85th minute, before Maureen Khakasi completed the comeback in the 90th minute.
The two teams face off again in the return leg on September 29 at the Kenyatta Stadium, Machakos. Should Kenya prevail over Ethiopia, they will enter the tournament's second last qualification stage where they will face either Algeria or Ghana.
The Kenyan youngsters thrashed Bostwana 7-1 in their first leg of the qualifers two months ago at the Lobatse Stadium in Botswana, before the Southern Africans pulled out of the second leg.