After the restart, Rise and Shine made changes and brought in Charlton Mashumba, who grabbed their second goal in the 78th minute and Polokwane went on to secure the maximum points via a 2-0 win.
As a result, City are placed fifth on the league table with 36 points from 23 games, while Arrows are placed 10th with 25 points.
Although Baroka netted first courtesy of Mduduzi Mdantsane, the hosts bounced back and claimed a win.
Sello Motsepe's goal on the stroke of half-time and a 52nd-minute header from Mothobi Mvala ensured that Highlands Park returned to winning ways and they remained ninth on the league table with 29 points.
Baroka coach Wedson Nyirenda was left furious following the defeat and his side remained 13th on the log with 21 points.
However, Usuthu found the back of the net through Bonginkosi Ntuli three minutes after the break to put the hosts in the lead.
With Wits searching for the equaliser, AmaZulu capitalised at the back with Somila Ntsundwana picking Ovidy Karuru with a cross on the far post and the Zimbabwean made it 2-0 in the 81st minute.
The result dented Wits' hopes of winning the PSL title as they remained fourth on the log with 38 points from 23 games.
AmaZulu climbed up to the 10th spot with 26 points from 23 matches as they look to qualify for next season's MTN8 Cup.