Sundowns won the game 3-1 in Umlazi, Durban to maintain their four-point lead at the Premiership summit with seven matches remaining.
The PSL's disciplinary committee have charged the hosting side for failing to ensure adequate safety and security at the venue.
A hearing has been scheduled for March 14.
The League released a statement, which reads: 'The Premier Soccer League Disciplinary Committee has charged AmaZulu FC for contravening the Safety and Security Manual (Compliance Manual) during their Absa Premiership fixture against Mamelodi Sundowns on Friday night, 02 March 2018.
'This is after a section of supporters at King Zwelithini Stadium starting to throw objects on the field resulting in the game being stopped for about 10 minutes by the referee.
'AmaZulu will also face a charge of failing to provide adequate security personnel at their game as required by the Compliance Manual.
'They will appear on 14 March 2018.'