His five-man misfiled stifled Kilmarnock, meaning neither goalkeeper was forced into a meaningful save in the first half.
It was Saints who had the best chance of the turgid first period, John Sutton firing wide from seven yards in the seventh minute.
There was more urgency in the home side thanks to a couple of contentious decisions by the far side linesman, including disallowing a Steven Naismith effort and they took the lead in the 54th minute.
Allan Johnston clipped the ball over a static defence for Paul di Giacomo to beat the offside trap, and the striker showed good composure to wait for Tony Bullock to commit himself before calmly chipping the ball into the net.
Killie almost added a second two minutes later when Naismith ended a free-flowing move on the right wing by heading Danny Invincibile's cross against the crossbar.
MacPherson made an immediate change bringing Mark Corcoran and Richard Brittain into the action and the pair produced an equaliser in the 75th minute.
Brittain measured a great pass through the defence for Corcoran to race on to. The winger got the break of the ball as he challenged Fraser Wright and was delighted to see it spin over keeper Graeme Smith for the leveller.
Colin Nish and Invincibile both wasted good chances for Killie and di Giacomo shaved the post in the last minute.