The Arua side will now play Entebbe in a two-legged semi-final in June.
Onduparaka 1 Soana 0
Semi-final first leg on June 8
KCCA v Vipers
Entebbe v Onduparaka
Return legs for June 12
Captain Muhammad Shaban scored the only goal as new premier league entrants Onduparaka dumped Soana FC from the Uganda Cup on Thursday.
Soana goalkeeper Muhammad Didi was sent off in the game played at Green Light Stadium, Arua.
The Arua side will now play Entebbe FC in a two-legged semi-final in the first half of next month.
Meanwhile, KCCA FC and Vipers FC will face off in other semi-final.
Kampala region will host the final this year at a venue yet to be named.
SC Villa beat KCCA FC 3-0 in the replay to win last season's competition. The winner of the Uganda Cup represents the country in the CAF Confederation Cup.