Following their slow start, the closest they came to scoring involved Gustavo Paez, whose cross-cum shot was easily dealt with by George Chigova in the opening 10 minutes.
It was the Limpopo who looked settled early on, taking on the Amakhosi defence with their pace while testing Itumeleng Khune with shots from afar in the opening quarter.
In quick succession, Wiseman Meyiwa looked to give the hosts the lead with shots from range, his first being parried away by Chigova for a corner and his second a first-time volley from the resultant set-play.
A foul on dangerman Rodney Ramagalela resulted in a free-kick from 30-yards, Walter Musona stepped up to beat Khune hands down to give the visitors the lead.
He looked for his second after beating the offside trap, but Khune raced off his goal-line to thwart him in his tracks a minute later.
The Rise and Shine looked threatening on the counter, but were given a scare with Siphiwe Tshabalala’s long range effort forcing Chigova to flick it away for a corner with his legs.
Tshabalala’s delivery led Ryan Moon to sneak ahead of the Polokwane defence to draw Steve Komphela’s charges level a minute after the half and hour mark.
The goal brought the Glamour Boys into their spark and Tshabalala almost gave them the lead, but his header from Philani Zulu’s arrowed ball went wide in the 33rd minute.
At this stage, City were rattled and had no answers to combat the interplays of Tshabalala, Paez, Zulu and Moon.
The Amakhosi started the second half on a different note, applying the early pressure and caught the Northern Province side wanting on a few occasions.
Equally so, City asked questions of their own as they looked to regain the lead, but were undone by a lack of timing in the final third.
They almost went ahead, but Rendani Ndou’s goal was controversially ruled out for offside by the officiating team.
New signing Siphelele Ntshangase came on for his debut, which was followed by the introduction of Dumisani Zuma as the Amakhosi looked to seal up the contest.
Zuma connected perfectly with a Joseph Molangoane cross to give the Amakhosi the lead for the first time in the match after 65 minutes.
That proved to be enough to seal all the points for the Amakhosi, who returns to fourth spot.