"It was taken out of our hands," said Brown.
"The referee has made a diabolical decision. The manner of the penalty is a shocking decision."
With 15 minutes of the match at Dens Park remaining and the home side holding on to a one-goal lead, Aberdeen's Peter Pawlett drove into the box and went down under a challenge from Lewis Toshney.
Referee Muir pointed to the spot and Niall McGinn blasted the ball into the top of the net to level the scores, with the match ending in a draw, meaning St Mirren, seven points ahead, could no longer be caught with only two games remaining.
Brown was stark in his criticism of the penalty decision and felt his players deserved more from their efforts on the day against Aberdeen - and also in the recent run-in with the Paisley side as Dundee attempted to stave off the drop.
"It's our livelihoods, and people forget that," said Brown. "We didn't feel as though Aberdeen were a threat, we felt as though we were coping well enough - and that decision leaves a bad taste in the mouth.
"If it had been a wonder-strike from 30 yards or brilliant play, then you would take your hat off and concede it.
"When it happened, I could see from half the pitch away it was never a penalty. You can see it was a two-footed dive, but the referee gave a penalty.
"I mean, come on. He can go to his work on Monday morning, but we've got to come back in and pick the pieces up.
Play media"So whoever is in charge of the referees wants to have a hard look at them."
The decision yet again raises the question of the live use of television evidence during matches and Brown insists it should not be left to one man to make a decision which can affect the lives of players, coaches and fans.
"It's the players' livelihoods - they have to pay their mortgages," said Brown.
"We're down a division and they're out of a job because of an official's bad call.
"I'm very bitter at the moment, because the guys in the dressing room gave me everything, and they deserve better from officials.
"If there is a decision to be made like that, could they not take the 30 seconds to get to a monitor to check it?"
As full-time manager of the club, Brown must now consider his plans for the forthcoming season under the influence of a considerably reduced budget and a different football arena, but he insisted his players deserve praise for their recent fight-back.
"I'm very proud of my team, and the fans have backed us," said Brown.
"It's just a bitter taste to leave in the mouth with getting a draw and going down because of that decision.
"I hope I can keep the majority of them, but they will have impressed so much that I'm sure there will be other Premier League sides and teams down south thinking they can offer them a better deal than I can."