St Mirren new boy Adam Campbell gave the visitors the lead after 17 minutes as he made his first start since securing a six-month loan switch from Newcastle. The 18-year-old's debut strike was cancelled out when Killie midfielder Rory McKenzie level proceedings just before the half-hour mark.
The second half was an open affair but neither side looked as though they had enough to win it until Boyd scampered clear of the Paisley defence to flash home his 12th goal of the season and clinch a 2-1 win.
The victory sees the Ayrshiremen leapfrog their beaten opponents in the Scottish Premiership table to claim eighth place.
A quiet opening period was almost enlivened after 13 minutes by a powerful strike for the home side as Marc McAusland's misplaced clearance from Boyd's cross fell to Craig Slater on the edge of the Saints box. After taking an immaculate first touch he lashed a fierce strike toward the top corner but saw it come back off the junction of bar and post.
But it was Saints who made the most of their first opportunity 17 minutes in.
Jason Naismith did well to dig out a cut-back from the right flank as he found Campbell 15 yards out. The Newcastle recruit then drew in two Killie markers before swivelling and sending a low shot past home keeper Craig Samson.
It was a perfect start for Saints new signing but the lead last just 11 minutes as Chris Johnson fed McKenzie on the corner of the box. The midfielder settled himself before beating Marian Kello at his near post with a powerful drive.
Saints nearly hit back with an immediate response of their own as Conor Newton robbed Lee Ashcroft before squaring for stand-in skipper Steven Thompson but Samson did well to turn the shot away for a corner.
The former Buddies number one then had to react smartly as Paul McGowan's 18-yard strike skipped up off home forward Michael Gardyne's boot, forcing Samson to change direction before saving down to his left.
Referee Brian Colvin turned away Saints penalty claims with five minutes of the half remaining as right-back Naismith appeared to be flattened by Manuel Pascali as he galloped into the box.
The second period began with both sides cancelling each other out in the midfield.
But three minutes before the hour mark, Darren McGregor's slip let in Boyd. The former Scotland striker brushed off McAusland as he closed in on Kello's goal but could only balloon his shot over the target.
Seconds later, McGregor then made amends for his mistake with a fantastic last-ditch tackle just as Boyd looked set to strike again after Slater sent him sprinting in on goal.
At the other end, McAusland sent a header just wide from McGowan's clipped cross, while Samson blocked well from Danny Grainger's back-post volley.
Killie boss Allan Johnston sent on 17-year-old Robbie Muirhead for Gardyne after 66 minutes and the youth-team graduate soon had Kello worried as the Slovakian stopper was forced to gather his well-hit 25-yard drive at the second attempt.
The substitute then led a four-on-three breakaway with seven minutes remaining but made a mess of his shot after combining with McKenzie as the teenager swung at fresh air.
However, Muirhead regained his composure in stoppage time as he played a perfectly weighted pass for Boyd to sprint onto after beating the Buddies' off-side trap. The ex-Rangers striker kept calm as he fired under Kello to clinch the victory.