An own goal from Hearts captain Danny Wilson and a Michael Gardyne strike either side of Boyd's double were enough to see off the bottom side, who rallied through Dale Carrick and Sam Nicholson.
The victory eases Kilmarnock's relegation play-off fears, and Johnston was delighted with the performance of the 30-year-old, who is enjoying his second spell at Rugby Park.
Johnston said: "He seems to be getting better with age, doesn't he?
"I was here the first time he was here and I think he's actually playing better than he was then before he moved on.
"So that just shows you the type of form he is in and he's a massive player for us, in his general all-round play and his goal scoring."
Johnston also praised Boyd for carving out the crucial second goal, beating Jamie Hamill to a loose ball before holding off the Hearts midfielder to finish low past Jamie MacDonald.
"He's strong as well," Johnston said. "He's used his strength to hold him off and it's typical Boydy; you give him a chance and he scores. He's always in the right position."
Hearts manager Gary Locke, who tried to bring Boyd to Tynecastle in the summer, agreed that the striker made the difference on the day.
"I think it was clear for all to see," said Locke. "I know him well and in the three games we've played against them this season he's been the difference between the teams. There's no doubt about that.
"There's no point in looking to the past but he was certainly a player I would have loved to have brought to Hearts.
"Obviously the summer put paid to that with everything that went on. But I think you saw there that he's got a lot of qualities and he's been the difference between the two teams."