After a goalless first half, Relebohile Mofokeng broke the deadlock with his strike on 51 minutes.
Bonginkosi Dlamini levelled for Rise and Shine with 85 minutes on the clock but Patrick Maswanganyi secured the massively important winner just four minutes later.
The result meant that Ouaddou's side kept pace with Mamelodi Sundowns, who beat Golden Arrows 2-1 in their Betway Premiership encounter on Wednesday.
Pirates ended the evening in first place on the league standings with 44 points from 19 games, ahead of the Brazilians on goal-difference.
Speaking after the game, the Bucs boss said he couldn't understand why the stadium was still in use, telling SuperSport: "Let's congratulate the boys, it's not easy to win in Polokwane.
"We know it's a strong team, very compact, they're playing with braveness and the pitch didn't help us today."
"In that case sometimes I don’t understand, we have a magnificent stadium next to this stadium, and it's the image of the PSL, because the PSL is the best league in Africa.
"I think we have to put the teams in the right conditions to play."
Ouaddou added that he was proud of the way his team managed to scrape out a win in difficult conditions.
"But coming back to the game, we were very brave, we wanted to score but unfortunately we didn’t. But we created so many chances," he said. "I will say well done boys.”