It was an improved scoreline for the top-flight side on last season when the teams met in the Last 32 as well and they won 2-0, with Puleng Tlolane bagging a brace of goals on that occasion.
He grabbed another one in the first half of this fixture, before the victory was made safe by a superb second from Polokwane’s Zambian midfielder Salulani Phiri.
He blasted the ball home from 35-yards with a thunderous strike with the outside of his boot.
Just before that goal All Stars had come close to an equaliser when Thomas Kgope struck the crossbar with a superb strike from the edge of the penalty-area. Sipho Jembula also struck a post late on for City.
Walter Musona, younger brother of former Kaizer Chiefs striker Knowledge, grabbed the third late on.
There was still time for All Stars to grab a consolation as Thapelo Tshilo conceded a foul in the box and Mohau Motaung netted from 12-yards.
The victory is the first in seven matches for City since they beat Chippa United in mid-December.
It ends a run of five consecutive draws, four of which had been by 1-1 scorelines.
Polokwane City: Chigova, Semenya, Hlongwane (Maluleka 60'), Mbonani, Tshilo, Vilakazi, Mngomezulu (Jembula 72'), Phiri, Ndou (Musona 82'), Tlolane, Klaas.
African All Stars: Dhlamini, Khalishwayo, Radebe, Mtsweni, Motaung, Mmuso, Gumede (Hlophe 55'), Tshikweta (Mbamba 63'), Mhlanga, Kgope (Filander 82'), Shabangu.