KCCA had taken a deserved lead in the 26th minute through Brian Aheebwa before URA drew level courtesy of Benjamin Nyakoojo in the 31st minute.
However, four minutes later, URA should have made it 2-1 but Ivan Sserubiri missed from the penalty spot after his well-taken strike kissed over the bar.
But it was not long as they took the lead in the 36th minute after Shafik Kagimu met a cross from Joackiam Ojera.
It beat goalkeeper Charles Luwango and made it 2-1 with the scoreline remaining the same at the half-time break.
In the second half, URA FC had good game control and maintained good shape at the back with Nyakoojo and Patrick Mbowa proving impenetrable.
The victory has moved URA FC to the top of the league with 11 points in five games while KCCA FC dropped to third on nine points.