The former Scotland striker struck the opener for Saints against his old side after 12 minutes before 19-year-old talent John McGinn added a second with 10 minutes of the first half remaining.
Thompson then wrapped up the scoring with a fourth two minutes from time.
The visitors won 4-0 at Tannadice the last time the sides met and arrived in Paisley full of confidence following a winning streak that had seen them blast 22 goals along the way. Yet they appeared to be intimidated by the Buddies' physical approach.
Ironically, it was United who finished a man down after Keith Watson was sent off just seconds before Naismith's goal for a crude tackle on young defender Sean Kelly.
St Mirren's record in front of goal of late has been lamentable. In the four league games that followed last month's win over Ross County they had neither scored nor managed a win.
However, the club presented Lennon with a late Christmas present just minutes before kick-off when they confirmed Newcastle's teenage striker Adam Campbell would be arriving on loan in time to face Kilmarnock on January 2.
In the meantime, Saints would have to make do with lone frontman Thompson for the clash with United - but the ex-Scotland striker quickly came up with the goods.
Paul McGowan lobbed a cross to the back post which was knocked down by Conor Newton - another loan signing from the Geordies - for Thompson to shoot on the swivel from 10 yards out and his finish was flawless as he found the bottom corner.
Amid the excitement of that rip-roaring opening, though, Goodwin got himself booked after cementing opposition midfielder John Rankin.
United now found themselves behind for the first time since losing to Inverness at the end of October but responded by immediately turning up the heat on Saints.
Thankfully for Lennon's men, keeper Marion Kello was a match for efforts from Stuart Armstrong, Rankin and Ciftci.
Goodwin's luck with the law saw Ross County boss Derek Adams famously dub him the 'Ghost' recently because of what he claimed were referees' inability to see his many fouls. He got away with another again though as he went unpunished after clattering into Ryan Gauld on the half hour, sparking a furious response from United manager Jackie McNamara.
With a full compliment still on the field, Saints were able to successfully open up United again as McGowan fed McGinn on the edge of the box. The teenager forced his way past Paul Paton, dummied Gavin Gunning and then slid the ball past the wrong-footed Radoslaw Cierzniak in the away goal.
But United came back quickly with a goal themselves as Gauld's pass was collected by Ciftci with his chest, who then fired off a quick shot which rebounded up off Kello. The spin of the ball took it towards his empty net as two last-ditch attempts from the Saints defence failed to keep it out.
Goodwin was continuing to involve himself in needless altercations so Lennon took the decision to exorcise the Irishman, replacing him with David van Zanten two minutes before the break before referee Bobby Madden did the job for him.
Saints were again lucky to escape a red card as Marc McAusland slid in hard on Gary-Mackay Steven at the start of the half.
United were piling forward but Kello pulled off another fine diving save to deny Rankin's long-range effort on 52 minutes.
But their hopes evaporated when Watson saw red for his late challenge on Kelly.
It proved even more costly as Naismith settled the match with Saints' third seconds later. The right-back made an early run in from the wing to latch onto McGinn's through ball and he used his strength to hold off Andrew Robertson before poking the ball past Cierzniak.
And Thompson struck again late on as he collected McGowan's cross before slamming it onto the top corner.