The hosts had fallen behind to a Billy Mehmet goal just before the half-hour mark of but fought back thanks to an early-second half goal from John Sutton - playing against his old team - and Malcolm's bundled winner just after the hour.
St Mirren's woe was complete 20 minutes from time when Franco Miranda received a straight red card after the assistant referee signalled that he had used an elbow.
Motherwell manager Mark McGhee had his side's forthcoming European fixture in mind as he made three changes.
Defender Stephen Craigan and midfielder Stephen Hughes, who both suffered knocks in the midweek' Co-operative Insurance Cup defeat, were left out of the squad entirely ahead of Thursday's UEFA Cup first-round second leg against Nancy.
Marc Fitzpatrick and Steven McGarry came into the side in their place, with John Sutton promoted from the bench due to Chris Porter's suspension.
Saints boss Gus MacPherson drafted in defender Scott Cuthbert for the injured Will Haining, while Hugh Murray, Jim Hamilton and Stephen McGinn dropped to the bench to be replaced by Dennis Wyness, Steven Robb and the fit-again Andy Dorman.
The game got off to a thrilling end-to-end start, Mehmet forcing home goalkeeper Graeme Smith into a second-minute save following a flowing move up the left flank involving Dorman and Wyness.
Motherwell responded by heading straight upfield where Sutton had a header from Keith Lasley's pass turned away round the left-hand post by goalkeeper Mark Howard - and from the subsequent Steven McGarry corner, Sutton's shot was blocked on the line.
Jamie Murphy then rolled an inviting ball from the right all the way across the face of goal, and Smith punched away Wyness' lofted drive from the right inside seven minutes.
The frantic tempo then calmed down after that blistering start, the next chance falling to Wyness, who sent a diagonal effort whistling narrowly wide of the left-hand post from a Robb corner in the 14th minute.
Saints had the majority of goal threats, Dorman lifting a close-range effort onto the roof of the net and Mehmet heading into Smith's arms from another Robb cross.
Motherwell had a shot on goal just after the midway point of the first half when David Clarkson picked up possession 25 yards from goal but drove his shot wide of the target.
It was St Mirren who found the net shortly afterwards, however, Mehmet opening the scoring by collecting another Robb cross from the left flank and checking into a better position in the box before coolly firing low into Smith's net.
Malcolm came close to equalising for the hosts with a free-kick 11 minutes before the interval, only to see his 25-yard effort tipped onto the bar by Howard.
Motherwell equalised within three minutes of the restart in all-too-simple fashion.
The hosts won a corner on the right which was delivered to the near post by Steven Hammell - and Sutton scored the easiest of goals against his former club by nodding home a free header.
Clarkson sent a low drilled effort from outside the area into Howard's arms after 52 minutes, and Sutton then won a free-kick just outside the edge of the box, which Murphy saw beaten away by the diving Howard.
However, Motherwell took the lead after 61 minutes. Murphy played a corner short to Hammell, who crossed into the box, and Malcolm was on hand to bundle the ball home from close range at the far post.
Miranda tested Smith with a diagonal drive from outside the box which the goalkeeper had to parry away from his right-hand post, but the hosts came even closer to extending their lead minutes later through Hammell.
The defender had a corner cleared and played back to him by Lasley before swinging in a shot which crashed off the underside of the bar and rebounded to safety.
Saints were reduced to 10 men in the 70th minute when Franco Miranda received a straight red card after the assistant referee signalled he had used an elbow when jostling with Sutton at a throw-in.
St Mirren's 10 men maintained their search for an equaliser in the closing stages but failed to trouble home goalkeeper Smith.
Motherwell continued to attack and earn a series of corners and the home fans believed they had a claim for a penalty when Lasley was flattened in the box nine minutes from time.
Clarkson was denied by the attentions of two defenders as he turned and shot on the six-yard line from a Sutton cross five minutes from time, while Murphy's impressive run in injury-time set up Lasley for a shot which was comfortably held by Howard.