Aubrey Ngoma, who received his maiden Bafana Bafana call-up on Thursday, netted with a free-kick in the opening exchanges for the Citizens.
Former Orlando Pirates striker Lehlohonolo Majoro doubled the advantage with a clinical finish soon after following a through-ball from Golden Boot winner Lebogang Manyama.
However, Rise and Shine responded with two goals from Jabulani Maluleke and Thabiso Semenya before the interval. Maluleke struck in the 18th minute from another free-kick, while Semenya turned home a pass from Sipho Jembula.
Sibusiso Mbonani then nudged the hosts in front in the 55th minute when he nodded home a corner from the influential Maluleke.
Vusimusi Mngomezulu made the game safe with 20 minutes remaining as he rounded off a smart passing movement.
The Citizens finished third on the table - earning a ticket to the CAF Confederation Cup - to add to their Telkom Knockout triumph in their first year of existence.
Polokwane City qualified for the MTN8 in sixth spot in the standings.