The defender, pictured right, was thrown on early in the first half and his 76th-minute strike ensured his side came out on top.
Saints dominated the opening period and felt they should have had a penalty when Boyd clattered into Steven MacLean.
The striker’s mood only grew darker when he was flagged offside as he found the net moments later.
Killie’s win saw them rise to ninth, while Saints stay fifth.
Boyd was introduced after Jonathan Burns suffered a broken nose. His first involvement saw him put off Steven Anderson as the Saints skipper looked to tap home Liam Craig’s corner.
Team-mate Souleymane Coulibaly let Craig go free to connect with Ricky Foster’s cross, but Killie keeper Jamie MacDonald made a stunning reflex stop.
The visitors found their feet after a shaky start, but teasing deliveries from Jordan Jones and Coulibaly found no takers.
And they were lucky not to be punished when Boyd took out Anderson in the box. Referee Steven McLean was standing just 10 yards away, but waved play on.
Saints striker MacLean had the ball in the net, but had his celebrations curtailed by the assistant’s flag before Murray Davidson pushed a shot wide.
Kilmarnock found themselves three on one, but Coulibaly wasted the chance when he delayed his pass so long Jones could not avoid running offside.
The second period took time to get going, though Kilmarnock’s Rory McKenzie came close to bringing it to life as he rattled a 25-yard effort past a post.
Kane headed at MacDonald from close range, but chances were scarce.
Boyd prodded home from five yards when Saints failed to deal with Jones’ in-swinging corner.
Saints sub Graham Cummins had one last chance to rescue a point, but was denied when Killie full-back Luke Hendrie darted back to his goal-line to produce a last-ditch block.