The former Scotland striker struck 20 minutes from time to take his tally to nine for the season and continue his impressive goal-every-two-games strike rate.
In-form teenage winger Chris Johnston contributed his third goal in four games for the opener after 41 minutes, but the hosts were pegged back soon after the break as Kris Doolan levelled for Thistle.
However, Partick - who have not won since beating Inverness on October 20 - paid the price for Steven Lawless' incredible empty-net miss when Boyd touched home from Jackson Irvine's shot to confirm the three points.
It was not a pretty encounter. Both sides struggled to settle amid early exchanges which saw the ball rattle about the midfield like a pinball.
It was a heavy touch by Stuart Bannigan that saw Kilmarnock create their first real opening after 12 minutes as Rory McKenzie gathered in the box before sending a cross-cum-shot across the face of goal. Team-mate Johnston threw himself at the centre but his effort was in vain as the ball flashed by the winger.
Johnston was caught on his heels again moments later as Boyd split the visitors' defence but Thistle keeper Scott Fox was there first to boot clear.
Partick quickly found their feet too and Craig Samson did well to recover when Doolan pounced on his half-hearted clearance from Aaron Taylor-Sinclair's low cross, with the home goalkeeper down smartly to block the striker's follow-up volley.
Boyd was similarly denied by Fox at the other end after 20 minutes as he wriggled clear of Gabriel Piccolo to fire off a shot, while Partick's James Craigen came close with a low drive that licked Samson's left-hand post.
Thistle may have struggled for goals recently - just three in the six matches before arriving in Ayrshire - but their passing displays have won plaudits. However, there was little evidence of quality from either side as the game flitted from one bad touch to another.
The driving rain and blustering wind hardly helped matters but the 3,865 fans watching could be forgiven for feeling short-changed as the game headed towards the break. Even Craigen's ambitious 40-yard free-kick attempt could only raise an ironic cheer as it sailed harmlessly into Samson's arms.
It began to look as though it would take a mistake to break the deadlock and so it proved four minutes from half-time as Kilmarnock got lucky.
Boyd failed to bring down Rory McKenzie's cross but his miscontrol broke kindly for Johnston on the edge of the box and the 19-year-old planted a low strike past the diving Fox.
But the hosts' lead lasted just four minutes into the second period as Doolan levelled.
Taylor-Sinclair lobbed a throw-in at the striker and Kilmarnock left-back Jeroen Tesselaar bought the 27-year-old's dummy as Doolan twisted one way before the other. That put him through on Samson and he gave the goalkeeper the eyes, passing a low shot into the left-hand corner while his opponent dived hopelessly to the other side.
Samson did better against Christie Elliot though as he palmed away an effort bound for the top corner just after the hour.
With the weather relenting, both teams set about keeping the ball on the floor. But it was a dodgy bounce which cost Lawless as he blazed over from Elliot's cross with an empty goal to aim at.
Fox had more luck when he spilled substitute Michael Gardyne's strike without finding a Kilmarnock player sniffing about the rebound.
But within seconds, the goalkeeper had been beaten as Boyd got the faintest of touches to Jackson Irvine's long-range effort, diverting it past the stranded Fox.
Kallum Higginbotham should have beaten Samson after combining with substitute John Baird but was denied at point-blank range, while the former Scotland squad member did just as well to push away Ross Forbes' free-kick as Kilmarnock held on for their fourth league win of the season.