However, the scoreline did not reflect the pattern of large periods of the match as Partick were again left with nothing to show for their dominance of a game.
Their misery was compounded with the dismissal of Stephen O'Donnell midway through the second half.
Conrad Balatoni was restored to the Jags' defence following Monday night's 4-0 reversal against Aberdeen, with Aaron Muirhead dropping to the bench.
Steven Lawless, who also missed the defeat at Pittodrie through injury, returned to the midfield at the expense of the injured Sean Welsh.
Lennon kept faith in young full-back Jason Naismith for the visitors, who continued in place of David van Zanten.
Marc McAusland was restored to defence in place of Lee Mair, who had started the abandoned match against Ross County last time out, and former Hearts goalkeeper Marian Kello continued for the visitors in place of the injured Christopher Dilo.
The home side started the match brighter and a fine early move down the Thistle right led to Lawless finding Stuart Bannigan inside the St Mirren area, the midfielder's effort blocked behind by McAusland.
Partick were getting some early joy down both wings, and Naismith was booked following a crude challenge on James Craigen to halt the wide man's progress after just 10 minutes.
O'Donnell had been getting forward to good effect for the home side in the opening minutes but the right-back was caught out at the other end when John McGinn muscled him off the ball.
O'Donnell's attempted recovery tackle led to a foul on McGinn 30 yards from goal and a deserved yellow card for the Thistle man.
Kenny McLean's dipping effort from the free-kick was scooped around the post by recent Scotland call-up Scott Fox, but the visitors took the lead from the resultant corner.
McLean's in-swinging corner found Thompson unmarked at the near post to head emphatically past Fox in the Thistle goal for his fourth of the season after 16 minutes.
The home side tried to find an immediate response, and Kallum Higginbotham fired just over from 20 yards before Aaron Taylor Sinclair's driven cross was turned behind by Darren McGregor.
The resultant corner by Higginbotham was only partially cleared, O'Donnell helping the ball back into the area where Kris Doolan's shot on the turn was saved well by Kello low to his left.
Partick continued to press for the equaliser and another Higginbotham corner caused problems for the St Mirren defence, his low ball being missed completely by Balatoni before being blazed over by Gabriel Piccollo when it looked easier to hit the target, meaning St Mirren preserved the lead at the interval despite the home side's dominance.
Thistle started the second half on the front foot, and a neat turn by Craigen inside the area allowed him space to get a shot away, his left-foot effort deflected behind by McAusland.
Thistle manager Archibald then made a tactical change, midfielder Christie Elliot replacing Piccollo, who had struggled to deal with the aerial threat of Thompson, and Isaac Osbourne taking the Mexican's place at the back.
The home side then had a huge claim for a penalty waved away by referee John Beaton, Higginbotham cutting inside to unleash a right-foot shot which clearly struck the outstretched arm of Saints captain Jim Goodwin. The referee deemed the contact was accidental but much to the fury of the home supporters.
Ross Forbes replaced Steven Lawless for Thistle and Van Zanten replaced Naismith for St Mirren on 66 minutes, and Goodwin was booked almost immediately afterwards for a foul on Taylor-Sinclair.
As the home side struggled to find a way through the stubborn St Mirren defence, John McGinn nicked the ball on the edge of his own area and drove towards the Thistle half.
In a repeat of the incident that led to the opening goal, O'Donnell fouled the winger from behind to pick up his second yellow card of the game after 70 minutes and see his side reduced to 10 men.
Just a minute later, St Mirren took advantage of the extra space afforded to them, with Paul McGowan cleverly feeding the on-rushing Conor Newton in the inside-right channel to drive into the box and finish through the legs of Fox to double the visitor's advantage.
Bannigan was then replaced by Muirhead as Thistle manager Archibald tried to re-organise his side, and Goodwin was replaced by Gary Harkins for St Mirren with 10 minutes remaining.
Gary Harkins replaced Goodwin for the final 10 minutes, and the Buddies put some gloss on the scoreline when another substitute, Danny Grainger, who had replaced McGowan, crossed for Thompson to control and finish with his left foot from 10 yards in the final minute.