On the back of a goalless first-leg draw in Accra, the teams played out a goalless draw in regulation time, but gave in within extra time through a spot kick.
Although Coach Mercy Tagoe-Quarcoo made three changes to the side that started at the Accra Sports Stadium last friday with Portia Boakye, Mavis Owusu and Elizabeth Owusuaa all earning starting places, the Black Queens could not live to expectation but rather had a sloppy start.
The Harambee Starlets started the contest on high note with lead striker, Nwahalima Adams finding spaces in front of the Ghanaian box but, most of her shots were denied by goalkeeper Fafali Dumehasi.
However, the Ghanaian side recovered possession from the hosts in the second half but couldn't find the net.
The game travelled beyond regulation time before Gentrix Shikangwa put the home side ahead through the spot.
This third round result means the Black Queens will miss the Tokyo 2020 Olympic Games.