Livi almost relegated thanks to us!!!!!!
Boyd's 18th of the season in the 75th minute and Johnston's strike 10 minutes later, consigned the Lions to defeat.
Livi must now avoid defeat against Dundee next week to be sure of preserving their top-flight position.
However, they were dealt another blow in the second period when defender David McNamee was carried off with an ankle injury.
Livi also went into the game on the back of two successive wins and after collecting 10 points out of a possible last 12 with just two SPL defeats since February - at the hands of Celtic and Hearts.
But their fine run was derailed by Jim Jefferies' in-form Kilmarnock, who moved into seventh spot with the win.
It took eight minutes for any kind of goalmouth action to develop, but Gabor Vincze's excellent right-wing cross was flapped away by Killie keeper Alan Combe for a corner.
From Burton O'Brien's delivery Combe was again dubious under pressure and Colin McMenamin turned the resulting loose ball into the net - only for referee Iain Brines to rule it out for a foul on the keeper.
Peter Leven's cross-shot on 15 was Killie's first real foray into Livi territory and, a minute later Gary Wales, who along with Garry Hay, signed a new deal before the game, played Gary McDonald in through the inside left berth.
Livi keeper Roddy McKenzie had to be sharp to smother the midfielder's effort.
Kris Boyd, back up front after a game on the bench against Dundee United, looked lethargic in the early stages, but went close with a snap-shot on 36 which flashed just wide.
The second half started as the first had ended and it took 13 minutes before either side threatened to break the deadlock.
Killie were looking the more dangerous, with Boyd in particular a threat and, after 67 minutes, the striker curled a fine effort just wide.
Moments later, David McNamee was carried off on a stretcher after appearing to catch his studs in the turf.
Killie took the lead their second-half play merited on 75 when substitute Murray's cross was volleyed towards goal by Wales and Boyd was there to add the finishing touch.
Steven Naismith was replaced by Johnston on 85 and the former Rangers and Hearts winger made the game safe with his second touch.
His first was when he controlled an intelligent knock-down from Wales before drilling the ball beyond McKenzie with his right foot.
Johnston, whose only two previous SPL goals this term coincidentally came against Livi, nearly made it 2-0 three minutes later, but his shot was deflected wide.