Nelsen had a lengthy exchange with the fourth official Saturday after his team failed to get a penalty call midway through the first half when striker Jeremy Brockie went down in the New York Red Bulls' penalty box.
The Toronto manager was still shaking his head after the MLS match, which ended in a 0-0 draw.
"These decisions are game-changers, aren't they?" said Nelsen. "They're absolute game-changers.
"He stood on his foot," Nelsen said of the Red Bulls defender. "It was so blatant. The whole crowd saw it."
Nelsen said the official explanation for the non-call by referee Jorge Gonzalez was that Brockie "reached his foot back so he could get tripped over."
"Jeremy Brockie's an intelligent man, but I don't think he's got eyes in the back of his head," Nelsen said dismissively. "If he did that on purpose, I'd be amazed. Again I'd rather they'd just say 'I made a mistake,' than come up with an excuse like that."
Brockie called the non-call "a stone-cold penalty."
"I asked the ref about it and he said he clipped my ankle but there was no intent. Whatever that means."
Nelsen has complained about MLS officiating before, including in midweek when midfielder Jonathan Osorio was brought down in a 1-0 loss at Chivas USA.
He called that one "the most stone-coldest penalty in the whole of the world."
After a 1-0 loss to visiting Real Salt Lake on June 29, Nelsen pointed to another missed Brockie penalty call.
"We had a stone-cold penalty and I was astonished why the referee did not give it," he said at the time.
There were also earlier complaints over missed penalty calls in games against New England and Philadelphia.
On Saturday, after offering his views on the latest non-call, the rookie manager tried to make light of the situation.
"I don't know if there's a curse. Have we cursed the referees that come here? They just refuse to give penalties. There must be something going on. (We'll have to) hang some garlic outside their office or something.
"Am I getting in trouble for that?"
Toronto FC president Kevin Payne complained earlier in the season that his team was seeing too many novice referees this season.
The MLS fined Nelsen and Toronto for violating the league's so-called mass confrontation policy for an on-field altercation in the Real Salt Lake game. Toronto FC had been warned for a violation earlier this season.