Gary Harkins dispossessed Jim Goodwin and drove forward before unleashing a stinging effort from 25 yards, which beat Craig Samson and rattled the right-hand post.
Some excellent work from Van Tornhout provided a good opportunity for Garry Hay but the midfielder's control let him down at a crucial time.
Hay turned provider as Killie opened the scoring on 13 minutes.
He rolled a neat through ball to Dietr Van Tornhout and the Belgian striker finished well.
Van Tornhout failed to add to his tally when he blazed well over the top after doing well to control Harkins' knockdown.
Against the run of play the hosts grabbed an equaliser after 23 minutes.
Thompson met Thomson's cross and his low shot slipped past Bell and into the net.
St Mirren appeared to find their stride following their leveller and only a tremendous piece of goalkeeping from Bell prevented Hasselbaink's curling effort from finding the top corner.
Bell came to Killie's rescue again when he made a brave stop at the feet of Thompson after a good delivery by Hasselbaink.
Hay struck wide of the target eight minutes after the restart as both teams made a slow start to the second half.
The hosts responded at the other end but were unable to profit from Paul McGowan's clever slide-rule pass.
St Mirren grabbed the lead on the hour mark when Imrie floated over an inch-perfect cross and Thomson rose to bullet a header into the bottom-left corner.
The home side stretched further ahead after 65 minutes when Hasselbaink seized on an error by Sissoko and then slotted the ball coolly beyond Bell.
The away side continued to show an attacking threat and Shiels was unlucky to see his cut-back deflected behind by James Dayton.
Hasselbaink almost capitalised on more hesitancy in the Killie defence but was denied by a good low stop from Bell.
Sissoko flashed a shot just wide of Samson's goal with 10 minutes remaining, but their day was soon to get worse.
Lewis Toshney slipped on the edge of the penalty area and Thompson curled a wonderful effort beyond Bell.
Shiels lashed a consolation goal home from the edge of the box, to give the large Killie travelling support a glimmer of hope, but they failed to take advantage of four minutes of added time and Saints held out for all three points.
Sandy's Match Pic's are HERE