Boyd struck as the clock ticked past 90 minutes to inflict a 2-1 defeat on the Buddies, who had taken the lead early on when on-loan Newcastle teenager Adam Campbell grabbed a debut goal.
Rory McKenzie levelled the scores after 28 minutes but Boyd, whose contract expires in the summer, gave another example of the type of finishing that has made his manager so reluctant to let him depart.
The Killie manager said: “If we get chances to Boydy, he will always score. He got one and was unlucky with a couple of others. That’s how much of a threat he was.
“Boydy knows how much of a big player he is for us. Hopefully, we can keep hold of our best players. We are looking to improve the team rather than lose our best players.”
Suspended St Mirren skipper Jim Goodwin’s place went to Magpies youth Campbell and the 18-year-old striker made the most of his chance as he stuck away the opener with a tidy turn and finish on 17 minutes.
The lead lasted until just before the half-hour mark, when McKenzie beat Marian Kello at the St Mirren keeper’s near post with a powerful hit.
The second half was an open affair but after Boyd failed to make the most of two decent openings, it looked as though
a draw was on the cards.
However, the 30-year-old Scotland striker is in lethal form and with stoppage time remaining, he latched on to Robbie Muirhead’s pass before thudding the match-winner under Kello and into the net.
St Mirren boss Danny Lennon said his players switched off at the death but said he had high hopes for Campbell.
“I thought wee Adam Campbell gave a great flavour of what he’s going to bring, not just for us but to Scottish football as a whole. He’s got lovely soft feet, a lovely touch and good pace.
“He’s going to grow in confidence. It will take him a bit of time to settle into our game up here but that performance from him today – and the goal that he scored – will give him added confidence along the way.”