Twenty-two year old goalkeeper Graham Smith also enhanced his burgeoning reputation in a scrappy match.
Even with Stevie Crawford leading the line, United posed little threat in attack, but former Ayr United striker James Grady should have given the visitors an early lead with a diving header four yards out, but his poor effort slid well wide.
Mark Wilson's 21st minute free-kick did bring a smart save from the Kilmarnock keeper when the ball deflected off the head of home full-back Garry Hay and was destined for the bottom corner until Smith reacted quickly to dive low to his right to touch the ball round the post.
While United were toiling, Kilmarnock offered little, gifting possession back to the visitors very easily and relying on set-pieces to threaten the United goal, and it was from one such move that Killie crafted the opening goal.
Peter Leven flighted a free-kick perfectly for Boyd to power a header past the helpless Tony Bullock.
United had a glorious chance to level the match before half-time when they were awarded a penalty. Grant Brebner was sent sprawling by Freddy Dindeleux in the 42nd minute, but again Smith rose to the challenge diving full length to his left to parry Wilson's spot-kick.
The danger wasn't over for Killie, though, as Grady drove the rebound across goal, but James Fowler had covered his keeper and cleared from the goal-line.
The second half was as fitful as the first with neither goal threatened until the 66th minute when an intelligent pass from Colin Nish sent Boyd clear, but Bullock did well to block with his legs.
The best action of the match came a minute later. Teenager Steven Naismith smashed a great shot from the edge of the box that dipped and swerved, but Bullock stuck up his left arm and produced a stunning stop.
Killie had stepped up a gear now and Nish was the provider again in the 74th minute with a great ball for Naismith, but the youngster couldn't hit the target.
Killie sealed the victory in the 78th minute thanks to Boyd's 16th goal of another prolific season. The striker showed nerves of steel after Gary McDonald's driving run was halted illegally by a combination of Billy Dodds and Barry Robson.
Having missed from the spot last week, Boyd made no mistake this time, drilling the ball in off the post.
He could have had another hat-trick against United, but the linesman ruled him offside.
Killie weren't to be denied the third and Danny Invincibile fired an unstoppable shot into the far corner with three minutes left.