'Domingues' was notably benched for Wits' 2-1 victory over Pirates in their MTN8 quarter-finals on Saturday, despite getting on the scoresheet against Kaizer Chiefs in midweek.
Hunt revealed that the Mozambican midfielder was left frustrated but further explained that he needs to protect his more experienced players from injury and burnout throughout the season.
"You know he [Pelembe] is upset with me, but I want him to be upset with me - that's good," Hunt told reporters after the match.
"He scored a goal on Tuesday; he was brilliant on Tuesday but I left him out the team [on Saturday].
"He says 'why?' I say 'because you're 45-years-old and we need to manage you', you know, in the sense of [his age and how much he plays].
"I said to him, 'you'll definitely play, I just can't say when and how' and he came in for 20-25 minutes and he was great."
He added: 'He was fantastic. That's what it's all about. We never had that luxury last season, and it's important for us [to manage the squad]."
Wits will resume their domestic campaign after the international break when they face Cape Town City in the MTN8 semi-finals on the weekend of 10/11 September.