St Johnstone won a dour encounter at McDiarmid Park to move into fourth place in the Scottish Premier League.
Saints had the best chance of a poor first-half, Killie keeper Cammy Bell deflecting a Steven MacLean shot wide.
The home side took the lead when Murray Davidson slotted the ball home from close range as the Killie defence failed to clear a corner.
Kilmarnock couldn't find a way past the Saints defence and Gregory Tade's late header sealed the victory.
Both Steve Lomas and Kenny Shiels had targeted 47 points as the figure they needed to make the top six and therefore this was a big three points for St Johnstone.
The home side were better throughout and had the best of a fairly dull first period which saw Rowan Vine fail to take two real chances - the first when his shot was blocked and the second when he blasted wildly over the top from 12 yards after good set up play from Murray Davidson.
However, the best chance of the half fell to Steven MacLean when he was played in by Hasselbaink but Killie keeper Cammy Bell blocked his shot and the ball drifted just past the post.
Kilmarnock had been forced to hit on the break and William Gros had a shot saved by Alan Mannus in the Saints goal and Ross Barbour shot high and wide after a good run, but the 2425 people who had braved the cold to watch the game were far from happy and there was muted boos as the sides left the pitch at the interval.
The pattern continued after the break and Sammy Clingan fired a shot just past the post for the visitors before the home side took the lead on 57 minutes.
Dave Mackay's charging run and shot was deflected wide and Liam Craig's deep corner was not dealt with by the Kilmarnock defence and fell to Murray Davidson who blasted home his seventh goal of the season from eight yards.
Craig's delivery was to make all the difference again as Saints clinched the points five minutes from time, when his deep cross found substitute Gregory Tade free in the box and he flashed a header from eight yards past the keeper for his fifth goal of a frustrating season.
Killie boss Shiels was waiting for answers from his defenders about the loss of both goals long after the match, but the home side go into a three-week break with high hopes of a top-six finish and some of the fans even dreaming of another shot at Europe.