Mbuthuma put Pirates ahead in the 4th minute, finishing off Mofokeng’s assist just after Otladisa had hit the post for Gallants.
The result left Sundowns second in the group on nine points, trailing leaders Al Hilal by two.
Orlando Pirates chase more silverware with eyes on league and Nedbank Cup
The controversy emerged after Sundowns placed analyst Mario Masha on suspension pending an internal investigation, following reports that he shared sensitive tactical details with Mokwena ahead of the Group-stage clash in Pretoria.
Betway Premiership weekend action sees Polokwane City host Siwelele at Peter Mokaba, Chippa United welcome Richards Bay to Nelson Mandela Bay, and Sekhukhune United face Orbit College at Makhulong.
Sekhukhune United goalkeeper Renaldo Leaner says there is real belief at the club that they can challenge for the Betway Premiership this season.
With qualification not secured, the Soweto giants face a stern examination away from home in the final round of group fixtures.
With qualification still in doubt, Masandawana are preparing for a must-win CAF Champions League Group C encounter against MC Alger that could define their continental campaign.
Kaizer Chiefs team manager Bobby Motaung says the club felt it was unnessary to sign a raft of players during the January transfer window.
Analyst Mario Masha has been suspended by Mamelodi Sundowns for allegedly leaking information to former coach Rulani Mokwena’s MC Alger.