Sundowns beat University of Pretoria 2-1 on Saturday to advance to the Telkom Knockout quarter-finals.
With his team leading in extra time, Mosimane instructed defender Wayne Arendse to warm-up - prompting boos from the home crowd.
Mosimane then decided against fielding Arendse, instead bringing on Asavela Mbekile for fellow midfielder Teko Modise in the 113th minute.
"I think I heard the noise but I was not sure what was happening," said Mosimane when asked about the incident.
"I didn't know they were booing Wayne, it's not good. We can't tolerate people who boo their own players if that was the case."
Mosimane insisted he is his own man when it comes to calling the shots in the dugout.
"We can't control the grand stand. About the sub, if Teko has a hamstring problem, we have to put in Mbekile.
"I am not sure about the booing but if I think the [substitution] is the only way for us to go through to the next round, I would have done it and you know I will do it," he concluded.
Meanwhile, a Downs supporter at the venue explained why they were unhappy to see Arendse preparing for action.
"We had to voice our displeasure at the defensive sub. There was no need to defend but to attack.
"I am glad he [Mosimane] listened to us," said the fan, who wished to remain anonymous.