Gary Locke's men went down 2-0 at Rugby Park after the former Scotland frontman struck once in each half.
The Jambos - deducted 15 points for entering administration in the summer - had clawed back the deficit on their rivals St Mirren to just nine at the beginning of this month but the defeat to Killie now means they must start all over again.
The victory is Killie's second in succession thanks mainly to Boyd's instinctive finishing capabilities.
Scotland defender Danny Wilson was at fault for the opening goal as Boyd stuck the opener. Collecting Sean Clohessy's pass on the edge of the box, the former Rangers man still had work to do if he was to threaten but Wilson's slip opened up a path to goal as Boyd then calmly took his time, dummied Jordan McGhee and then fired past Jamie MacDonald in the Hearst goal.
Boyd came up with his second of the afternoon following the break. Brad McKay was caught ball watching underneath Clingan's long free-kick and Boyd took one touch before clipping it over MacDonald from a tight angle.
Late goals from substitutes Scott Vernon and Gregg Wylde gave Aberdeen a deserved 2-0 win over Hibernian at Easter Road and moved the Dons into second spot behind Celtic.
Wylde, who had come on for Peter Pawlett and set up Vernon for his goal, wrapped up the points with a breakaway effort in the second of four minutes added time with his first goal for Aberdeen since signing for the club in the summer after leaving Bolton.
An entertaining, end-to-end game became increasingly scrappy in the closing stages but when Vernon took a pass from Wylde, he slammed it high past Williams before taking the acclaim of the Red Army behind the goal.
Those fans held their breath in the 86th minute when Langfield slipped to give the ball straight to Collins but the Hibs substitute curled his shot past the far post.
However, in injury time, Wylde popped up to allay any fears of a late leveller when he drilled the ball past Williams and into the far corner.
Dundee United returned to winning ways in style as they outclassed St Mirren 4-0 in a one-sided match at Tannadice.
Nadir Ciftci's first-half double put Jackie McNamara's team in the driving seat before Ryan Gauld and substitute Chris Erskine broke through in the second half.
It was a day for Danny Lennon's visitors to forget, especially with fellow relegation rivals Kilmarnock winning.