It is a result that extends Ghana's absence from the U-17 World Cup into a ninth consecutive year.
Ghana came flying out of the blocks. Eric Gyamfi gave the Black Starlets the lead after just nine minutes, rifling a shot through the legs of goalkeeper Lukyamuzi after being left unmarked at the back post.
Uganda responded by switching to a three-back formation, and the tactical adjustment began to show its effect almost immediately. Captain Mukise then scored directly from the resultant corner kick to draw level twelve minutes before the interval.
Abdul Latif gave Ghana the lead in the second half after pouncing on a loose ball, the goal created by Gyamfi, whose cross from the left was beautifully dummied by Clement Agyei, leaving Latif to stab home.
Ghana were in the lead with the clock ticking down. Victory, and a place at the U-17 World Cup, appeared to be within touching distance.
On the cusp of full-time, Uganda coach Laryea Kingston asked the referee to review a handball incident in Ghana's penalty area.
The referee obliged and, after a quick review, pointed to the spot. Replays showed that Ghana right-back Nicholas Asumang had handled the ball from Mukise's cross.
Ibanda Arafat elected himself for the penalty and sent John Annan the wrong way to restore parity. The referee subsequently indicated 10 minutes of additional time, but neither side could find a winner.
Just before the match went to penalties, Ghana coach Prosper Ogum brought on goalkeeper Michael Armah for John Annan, and Mark Mensah for Nicholas Asumang, specifically for the shootout.
In the end, Uganda held their nerve when it mattered most, winning the shootout 8-7, sending Kingston and his players into jubilation and leaving the Black Starlets heartbroken on the turf.
Kingston, the former Black Stars midfielder who delighted fans for years with his energy and skill, and who once coached Ghana's U-17 side himself. Now, as Uganda's head coach, he has denied Ghana a World Cup place.
It is only the second time Uganda have qualified for the FIFA U-17 World Cup, having achieved the feat last year.
Ghana's absence from the U-17 World Cup now stretches to nine years. For a nation that won the competition twice in 1995 and 1999 and was once the most dominant force in African youth football, that statistic is a sobering reflection of how far the conveyor belt has fallen.