The former Scotland man scored in the 16th minute and again in the final minute either side of a Conor Newton strike to ensure the Paisley men left Firhill with all three points, despite coming under pressure for large parts of the game as Thistle dominated possession.
The win sees St Mirren move into ninth place and close to within two points of their eighth-placed hosts, whose miserable day was rounded off by a red card for right-back Stephen O'Donnell with the score at 1-0.
Partick were also denied what was a strong claim for a penalty just before O'Donnell's dismissal, but McGregor preferred to focus on the contribution of his experienced team-mate as St Mirren sacrificed some of their passing principles to use Thompson's ability as a target man to good effect.
"There are very few games that I can remember where he's been dominated in the air," said McGregor.
"He wins more than he loses, so I think if you've got an asset like that you need to use it. And he's got great runners off him in [John] McGinn and Conor [Newton], so it's an asset and starting to use that is paying dividends."
The striker himself preferred to turn the attention back on his team-mates and insisted the victory was down to the hard work of the side as a whole.
"I thought we were very disciplined," said Thompson.
"Our shape was fantastic and we all stuck to our roles very, very well. We created some chances on the counter-attack and obviously when they got a man sent off it became an awful lot easier. It was a massive three points for us against a very capable team.
"I think this week was a very different game for us, away from home against a team that is exceptional in possession of the ball and like to pass through the lines. I think it was about trying to stop their strengths and we managed to do that quite well, so I think we should be applauded for that.
"I think with other results we've managed to jump a couple of spots up the league, which is nice given the start we had, so we're obviously delighted."
Partick midfielder Isaac Osbourne defended his sides approach to the game and said they would find it difficult to abandon their ethos for a more direct approach as the visitors did on Saturday.
"I think we tried to do it one or two times today but it's not our way of playing. We like to play the game properly," Osbourne said.
"We're just going through a bad patch at the moment in terms of results and hopefully we'll get one soon and go on a run from there.
"The fans enjoy our football as well, that's why I think they're not giving us too much of a hard time at the moment considering our run of results."
- Sports & Recreation
- St Mirren
- Conor Newton