Boyd appeared to brush the Aberdeen defender off fairly with a shoulder charge as the pair chased Jeroen Tesselaar's long ball in the 12th minute of the Scottish Premiership clash at Rugby Park, but referee Craig Charleston blew for a foul as the striker lobbed Jamie Langfield.
Johnston said: "If you're going to give free-kicks for that, you would be stopping play every two seconds.
"Boydy just simply outmuscled him and it's a great finish after that.
"The ref felt it was an unfair challenge but it looked a definite fair challenge to me as it did the majority of the crowd from their reaction.
"It's a big moment and refs have got to get these decisions right because it changes games."
The wind had played a major factor in the game, allowing Killie to dominate in the first half and Aberdeen after the break, although both sides had chances in each half.
Johnston was frustrated that his side could not take one with Langfield saving well from Boyd just after Dons midfielder Ryan Jack had headed against the bar, and Chris Johnston missing an excellent chance soon after.
Killie boss Johnston, who was without Jackson Irvine through illness, said: "It's frustrating. We had a couple of other chances first half and it's come back to bite us.
"Second half they pushed us back, mainly because it was difficult to get out with the wind. But I thought we dealt with set-pieces well, so it was frustrating to lose a goal from a corner, especially from a free headers."