The Black Queens have their 2020 Olympic Games dream cut shot after being eliminated by Kenya in the third round of the qualifications.
The Harambee Starlets beat Ghana for the very first time with a 1-0 victory in a second leg tie after extra-time.
The first leg ended 0-0 in Accra four days ago.
Gentrix Shikangwa scored the match winner for the Eastern Africa side in the 99th minute through a spot kick.
Ghana join South Africa and Nigeria to bow out of the journey to next year's Olympic Games in Tokyo, Japan.