The Scotland international curled home a free-kick with five minutes left after Saints had come from behind to take the lead in this Clydesdale Bank Premier League match.
Conor Newton's long-range strike had cancelled out Michael Higdon's 23rd goal of the season and Lewis Guy struck in the 75th minute after Motherwell had come close on numerous occasions in the second half.
But McFadden the final say to ensure Motherwell finished the weekend as they started it - three points clear of Inverness in second place and eight points ahead of the chasing pack in the race for a Europa League slot.
The hosts made a late change to their team with Zaine Francis-Angol coming in at left-back after Stevie Hammell tweaked his hamstring in the warm-up - and they got on top after the initial exchanges.
Well created the first real chance in the 10th minute when Chris Humphrey got to the byline and drove the ball across the face of goal but James McFadden could not convert and Higdon sliced wide when the ball flashed back across his body.
Nicky Law and Henrik Ojamaa then worked an opening after an exchange of passes but the Estonian was tackled just as he went to shoot and the ball trundled into the hands of Craig Samson.
St Mirren defender Marc McAusland found space at Sander Puri's corner but volleyed a difficult chance straight at Darren Randolph.
Motherwell were still on top though and they continued to probe for openings.
Higdon had another half chance after setting up a chance for Law to break forward. Law played it to McFadden who set over a first-time cross but Higdon's first-time volley was well over.
The home side took the lead in the 34th minute. McFadden picked out Higdon with wonderful vision and a measured cross but the ball would not drop and St Mirren cleared. But they could not get the ball far away and Keith Lasley delivered a perfect cross for Higdon to head across Samson into the top corner from six yards.
Saints tried to hit back and Steven Thompson's knockdown set up a McLean volley but the midfielder was under pressure and Randolph saved comfortably.
But Motherwell did not heed the warning and St Mirren were level four minutes before half-time.
The visitors kept possession on the right as they looked for an opening and Puri rolled the ball inside to Newton 25 yards out. Motherwell were slow getting out to him and the midfielder punished them by driving the ball across Randolph and into the top corner.
Both sides had further chances before the break, firstly when Law fired a first-time effort over the bar following a half-cleared free-kick. Higdon then lost McAusland at McLean's deep free-kick but the striker recovered to block the shot.
Motherwell created the first chances of the second half. Samson pushed Ojamaa's powerful strike over after a lay-off from Higdon, who headed wide under pressure from the resulting corner.
The home side continued in the same vein. McAusland defected Lasley's shot just over his own bar after some great skill by McFadden had instigated a break, and Samson pushed Humphrey's shot over after the winger had cut inside.
McFadden fired just wide from long range after more impressive close control and Lasley saw another shot deflected just over after Humphrey's break.
Law flicked Tom Hateley's mishit shot just past just before the home side were stung with 15 minutes left. St Mirren worked the ball through the heart of the Motherwell team and Guy finished slipped the ball past Randolph after a one-two with McLean had sent him through. It was the Englishman's sixth goal of the campaign but his first since October.
Motherwell looked set to be frustrated until McFadden conjured his second goal since returning to his first club in February.
McAusland was penalised for a challenge on Higdon 25 yards out and the former Everton winger curled the ball into the top corner with Samson only able to help it into the net.
McFadden had another free-kick saved, from a wider position, as St Mirren survived more late pressure.
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