Boyd volleyed home from the edge of the area in the 44th minute to seal a 1-0 victory for Killie in a match that Hibs needed to win to avoid an unwanted extension to their season.
Terry Butcher's men were sixth on January 2 after an Edinburgh derby win but another defeat left them in danger of joining capital rivals Hearts in next season's Championship.
Hibs have only taken four points from a possible 39, won one game since their new year derby victory, and they proved the fall guys in a five-way battle to avoid the play-off, despite beginning their post-split fixtures, which yielded just one point, in seventh place.
Killie defended a series of early corners for the hosts before Boyd found the net in the 13th minute, although the flag was already up when he latched on to Jackson Irvine's header.
Vitalijs Maksimenko got his head to a powerful first-time effort from Hibs defender Jordon Forster to divert it wide and Barry Nicholson cleared off the line after Scott Robertson glanced a header from Duncan Watmore's corner for the hosts.
Maksimenko then suffered a head knock that forced him off in the 33rd minute with Northern Ireland midfielder Sammy Clingan coming on and Manuel Pascali dropping to centre-back.
Killie enjoyed a good spell of possession which culminated in their opener and Boyd, making two yards of space, met Nicholson's driven cross to half volley the ball out of the reach of Ben Williams' right hand.
Hibs almost replied seven minutes after the interval when some goal-line defending repelled them during a frantic scramble following a corner.
Boyd wasted a good chance to extend Killie's lead when Ross Barbour's cross found him unmarked 10 yards out but Williams got down well to push his header away
Liam Craig then went agonisingly close to levelling minutes later, firing a powerful strike that cannoned off the underside of the bar and out.
But Williams saved well from Eremenko as Killie finished the game in the Hibs half and the Leith side now have until May 21 to find some confidence for a trip to Falkirk, Queen of the South or Hamilton in the first leg of their Premiership play-off.