Jim Jefferies' substitutions have proved critical in the last couple of weeks as Craig Dargo and Kris Boyd have come off the bench to score vital goals, and the Killie boss produced two more to make all the difference in this game.
Livi had the ball in the net in the first ten minutes when Colin McMenamin hooked home from Burton O'Brien's corner, but Kilmarnock keeper Alan Combe had been clattered, so the goal didn't count.
Moroccan international Hassan Kachloul then produced two pieces of Premiership quality by threading passes through the Killie rearguard. First he mesmerised Garry Hay and Peter Leven to send David McNamee bursting to the by-line. He cut the ball back on to a plate for David Lilley, but the striker dragged his shot badly wide.
He then had the composure and skill to delay his pass to McMenamin, but this time the young striker's touch let him down. However, the Moroccan then faded quickly from the game.
Killie threatened occasionally in the first half with Gary McDonald producing a good reaction save from Roddy McKenzie's stabbed effort and Steven Naismith went close with a waist-high volley from Gary Locke's corner.
Oscar Rubio had the best chance of the first half when he rose unchallenged to meet O'Brien's 28th minute corner, but he couldn't muster enough power to beat Combe low at his post.
Two Boyd snap-shots almost gave Killie the opening they looked for to secure seventh spot. First he rose to meet Hay's swinging cross but couldn't hit the target before an excellent turn and shot in the 65th minute shaved the post with the keeper stranded.
There was bad news for Livingston and for Scotland when McNamee was stretchered off in the 70th minute after falling awkwardly.
An inspired substitution by Jefferies led to the breakthrough. Little Stevie Murray replaced Leven in the 70th minute, and his first touch led to the opening goal.
He danced past the plodding Kachloul and sent over a cross which Gary Wales volleyed towards goal. His mis-hit shot wasn't goalbound but Boyd, who had laboured all day, popped up inside the six-yard box to touch the ball past McKenzie.
Jefferies made another change in the 83rd minute, and again the new man made an instant impact.
Allan Johnston replaced the industrious Naismith and linked with Wales a minute later as he used his first touch to fire the ball home off the far post. The pair combined again a minute later, but this time Johnston's powerful shot was blocked.