The game saw chances early on at Rugby Park, as Boyd was able to latch onto a long ball after five minutes, but he could not finish.
Just a minute later, Jordan Slew missed a decent chance for County.
On the half-hour mark, the deadlock was broken as Yoann Arquin fired Ross County into the lead, his fierce shot beating Craig Samson.
Just six minutes later, the visitors doubled their advantage as Yann Songo'o got a touch on the ball after Brian McLean's shot took a big deflection.
Killie were able to pull a goal back early in the second half, with Boyd driving through a ruck of players in the County box and firing a shot past the keeper.
Not long after the goal, Rory McKenzie nearly leveled with a shot that rebounded off the County post.
Midway through the second half, County were reduced to 10 men as Filip Kiss was sent off for picking up a second booking.
Killie equalised right at the death, Boyd's header breaking County hearts.