Kilmarnock took the points at a rain-lashed Love Street with a double by in-form striker Colin Nish.
Nish (centre) celebrates with strike partner Steven Naismith
After a lacklustre first-half, Nish broke the deadlock after 58th minutes, heading in Peter Leven's corner.
Kirk Broadfoot nearly equalised in the latter stages for Saints only for Killie keeper Alan Combe to deny him.
But Nish settled matters in the 78th minute when he was first to react after a sharp counter-attack involving Steven Naismith and Paul di Giacamo.
It was a very disappointing performance overall from the Paisley outfit as they ended their fourth successive game without a goal at home.
CIS Cup finalists Killie made four changes to their side, with Grant Murray and Gary Wales both injured and Simon Ford banned following his red card in the draw at Dunfermline.
Rocco Quinn dropped to the bench while Garry Hay, Alan Johnston, Di Giacamo and Ryan O'Leary all came in.
For St Mirren, Garry Brady and Alan Reid replaced David van Zanten and Eddie Malone respectively.
The Buddies were aiming to put some more breathing space between themselves and rock-bottom Dunfermline, and had the better of the opening stages with Killie's Hay clearing Ian Maxwell's header off the line.
Saints had the impetus and Stewart Kean got an acrobatic volley on target moments later but Alan Combe was well positioned to deny him.
The hosts continued to edge possession but Kilmarnock forwards Naismith and Nish were getting plenty of space on the break.
Leven forced Buddies' keeper Chris Smith to tip over his powerful effort after the ball broke to him on the edge of the box for the Ayrshire sides' best chance.
Johnston, in particular, started to threaten St Mirren with his trickery as Killie began to impose themselves on the game after a quiet start.
Nish (left) and Frazer Wright gave St Mirren a busy afternoon
Naismith tried his luck moments before the break with a snap shot but his effort went just over the bar, with the opening half ending goalless.
The second half failed to spark into life for the Love Street crowd - until Killie opened the scoring.
Leven swung in a corner and the ball was expertly met by Nish who powered a header into the roof of the net.
The goal was deserved on the balance of play for Jim Jefferies' men, although Nish received a yellow card for his celebrations by referee Collum.
Saints began to stir from their slumber with Broadfoot bringing a smart save out of Combe as they attempted to haul themselves back into the game.
But Gus MacPherson's men were caught out on the break, when, after putting too many players forward in search of a leveller, Kilmarnock struck.
Naismith picked up possession and cleverly found di Giacamo on the flank, and his ball found Nish lurking and the forward tucked the ball past Smith.
The second goal effectively killed the contest, and there was never any danger of the sluggish Saints making a concerted recovery as Killie comfortably kept control.
St Mirren: Smith, Reid, Maxwell, Broadfoot, Potter, Lawson (Mehmet 70), Brittain, Brady, O'Donnell (McKenna 85), Sutton, Kean (Corcoran 59). Subs Not Used: Hinchcliffe, Millen, Malone, Mackay.
Booked: Potter, O'Donnell.
Kilmarnock: Combe, O'Leary, Fowler, Hay, Frazer Wright, Nish, Johnston (Gibson 90), Greer, Leven (Locke 90), Naismith, Di Giacomo (Koudou 88). Subs Not Used: Smith, Lilley, Wales, Quinn.
Booked: Nish, Fowler, Johnston.
Goals: Nish 58,78.
Ref: W Collum