"I've no complaints about the penalty award," MacPherson told BBC Scotland. "It was never a free-kick before the ball gets played into the box.
"We'll ask questions regarding a penalty that we should've had."
Graham Carey and Andy Dorman netted to put the Buddies in command.
And Billy Mehmet claimed in vain for a penalty after coming into collision with St Johnstone goalkeeper Graeme Smith before the home side's comeback.
We took our chances. When you get into that situation, you've got to see the game out
Gus MacPherson
"Billy Mehmet's clean through; one-on-one," said MacPherson. "He knocks it by the goalkeeper and is taken out of the game by the goalkeeper.
"There was no decision given in that situation."
After Michael Duberry had pulled one back for St Johnstone, referee Charlie Richmond awarded a free-kick against Steven Robb for a challenge on Kenny Deuchar.
And, from that set piece, the ball was eventually volleyed towards goal by Murray Davidson and blocked on the line, seemingly by the hand of Stephen O'Donnell.
There was lengthy consultation between Richmond and assistant James Bee before O'Donnell was booked and Paul Sheerin converted from the spot to complete the scoring at 2-2.
"It's a handball, I think it was Stephen O'Donnell on the line," said MacPherson. "There is confusion because I don't think the referee or the linesman know who it was that was involved in the incident.
"My concern is the free-kick that was allowed to go into the penalty box.
"When Kenny Deuchar goes down, that is not a free-kick. There's no contact, there's no free-kick. Thereafter, we should clear our lines and it shouldn't be in that area at that point.
"These are massive decisions. It doesn't matter what stage of the season we're talking about. These are massive decisions that cannot go without talking about. Yet, we're told not to.
"We've gone to speak to the officials and we've heard that the referee felt injured in the last five minutes.
"He felt injured and thought he could get through the game but I thought that was a dangerous one if that's affecting his decision making. He had a leg injury.
"I'm not blaming the referee for that final incident. What we've had is some poor decision making elsewhere in the game, which would've given us the opportunity to go 3-0 up and see the game out."
The result moved St Mirren a point clear of Scottish Premier League bottom club Falkirk, who lost at Aberdeen, and level on points with Kilmarnock, who were beaten on the road by Hamilton.
St Mirren boast a superior goal difference to Killie, but MacPherson is frustrated that his side did not give themselves more breathing space in the fight against the drop.
"We've only got ourselves to blame," added the Buddies manager. "We played ever so well. We took our chances.
"When you get into that situation, you've got to see the game out. We've been in that situation before and yet we didn't see it out.
"But we've got to look at how that's not happened."
Source: BBC Sport
Source: BBC Sport