The visitors were two goals up by half-time, Steven Saunders' scrambled opener added to by John Sutton's header.
Ryan Stevenson forced Motherwell goalkeeper Darren Randolph into a save and Steven Saunders struck a Hearts post before half-time.
Motherwell were forced into a change when midfielder Keith Lasley succumbed to a hamstring injury and was replaced by Steven Saunders.
Goals by Steven Saunders and John Sutton gave Well their win in Edinburgh and ended a run of four straight defeats.
The victory came at a cost, though, with Keith Lasley and Steven Saunders both suffering injuries and Steve Jennings picking up a suspension.
Steven Saunders conceded a penalty in the 64th minute following a collision with Samaras, but Robson's spot-kick was parried by Ruddy to maintain the deadlock.
Both sides were forced into substitutions before the break with Odise Roshi replacing Ardit Shehaj for Flamurtari and Motherwell's Jonathan Page introduced for Steven Saunders.
Gannon picked out youngsters Shaun Hutchinson and Steven Saunders, who formed the central defence in Craigan's absence, for particular praise after the Scottish Premier League victory.
Silva missed the target with two further efforts before the Portuguese was closer to scoring with a goalbound shot that was headed clear by the alert Steven Saunders.
Motherwell ought to have taken the lead when Giles Coke failed to connect properly with a header and Steven Saunders could only turn the loose ball against the post.
Five minutes before the break Killie defender Frazer Wright was carried off on a stretcher suffering concussion after clattering into Steven Saunders and being caught by an accidental flailing arm.
Motherwell were without the suspended Steve Jennings and fellow midfielder Ross Forbes dropped out as Steven Saunders and Stephen Craigan returned to be part of a defence featuring four central defenders.
Yet the big Belgian had a good first half and made a superb save just before the break when Steven Saunders headed a Ross Forbes' free-kick goalbound, and had saved well from the same player earlier in the game.
The opener was not long in coming, with Boyd gathering a pass from Steven Davis with his back to goal before holding off Steven Saunders and spinning to drive the ball low into the far corner from 16 yards.
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