Brian Majwega scored on the rebound after missing on the first attempt from the spot to hand URA FC their first ever win in Mbarara and consequently sent them to the round of 16 in the Uganda cup.
The penalty was awarded after forward Ibrahim Dada had been fouled in the restricted area.
The tax collectors had played to a goalless stalemate with City in the first leg in Ndejje and any scoring draw could also send them through.
They managed to hold on to their lead regardless to seal a place in the next stage.
Mbarara city’s best chance at revival came in the 64th minute but they were denied by an acrobatic save from Nafian Arionzi.
URA join BUL, Maroons, Vipers and Proline to the exclusive list of the round 16 qualified teams.
Stanbic Uganda Cup Full-time Results
Mbarara City 0-1 URA
Busoga United 1-2 Vipers SC
MYDA 3-1 Proline
Maroons 6-0 Terrazo and Tiles
Luweero United Vs Onduparaka ( Not played)