The defeat dashed St Johnstone's hopes of leapfrogging Dundee United into the top six, remaining in seventh position, whilst the three points for St Mirren sees them restore the 15-point gap between themselves and Hearts at the foot of the table.
Equalisers from Steven MacLean, Nigel Hasselbaink and substitute Rory Fallon looked to have given the Perth side a draw, before former Scotland striker Steven Thompson grabbed the winner in the 89th minute to seal St Mirren's first home win of the season.
The St Johnstone players furiously protested the decision to send Wright off and award St Mirren a second penalty after Jim Goodwin had earlier seen one saved by Allan Mannus, and manager Wright thought they were harshly treated by referee Willie Collum and his officials.
"My instinct is that Frazer's one isn't a penalty, I think he's used his strength to stay in front of the player and nick the ball," said Wright.
"I believe the referee didn't give it, the linesman on the other side gave it, so we'll have to wait and see and watch it back on the DVD to see it clearer."
St Mirren midfielder McGowan, who was the player Wright was adjudged to have fouled, had a different view of the incident.
"The two of us were kind of tugging each other, but I'm going through on goal and obviously he's stopping me getting a shot on goal," he said.
"The letter of the law is that if you're the last man then you're off.
"Obviously you don't want to see players getting sent off, I would rather have gone on and scored myself, but that wasn't the case. These things happen and we'll take it."
St Mirren manager Danny Lennon heaped praise on his players after securing seven points from their past three games, paying particular tribute to two-goal midfielder McLean.
"I'm absolutely delighted with every one of them, but young Kenny McLean, I've got to single him out today," Lennon said.
"That's the third game in a row that he's brought that level of quality, and the energy that he brings - he's dynamic.
"The only thing that's been missing from his last two games was goals, and he's always been on the fringes of delivering that and I'm delighted that he's got his rewards today.
"The key thing for Kenny and everyone else that's got the jerseys right now is consistency."