Buhle Mkhwanazi was penalised for bringing down a City player inside the box, when it appeared the defender got to the ball first, before toppling the opposition player.
The result was put beyond doubt in the 90th minute as Thobani Mncwango netted the second for City, just moments before Tuks pulled one back from an own goal.
The win, nonetheless, ended a horror run of seven games without a win for the Polokwane outfit battling relegation.
Although not enough to lift them out of second-last spot in the league standings, the three points could go a long way in helping the Premiership whipping boys survive the axe at the end of their first season in the country’s top flight.
Rise and Shine find themselves 10 points clear of last placed Golden Arrows, who look destined for relegation when the league comes to an end in May.
An end-to-end start saw little in the way of chances for either side, until Tuks’ Geofrey Massa thundered a tricky effort on target and forced goalkeeper Modiri Marumo to palm away in the 16th minute.
Mpho Matsi threatened from distance, while Massa challenged in the air, as Tuks started finding their feet in their opponents’ half.
But their dominance counted for little as City took the lead in contentious fashion on the stroke of half-time, as Mkhwanazi was adjudged to have brought down a City striker inside the area.
Following furious protests from the Tuks bench and management, Mngqibisa teed-up the spot-kick, before dispatching past goalkeeper Washington Arubi to hand the visitors the half-time lead.
Trailing at the interval, Tuks went about getting back into the game, but were thwarted by a resilient City defence, bent on keeping a clean-sheet against a side they had already beaten earlier this season.
City looked hungry for more and when Mncwango was put through on goal, he made no mistake as he ghosted through the defence and slotted into the back of the net to see out the result, despite Tuks replying from the kick-off with a goal of their own.