Adam Rooney slammed in a penalty on 44 minutes after Glenn Loovens had clumsily upended Richie Foran.
After the break, two defensive blunders within seven minutes lead to replies from Adam Rooney and Jonny Hayes.
Meanwhile Craig Brewster reintroduced 20-year-old striker Adam Rooney to the Inverness team, while Ross Tokely was still missing through suspension.
Richie Foran slotted home Caley's opener and then set up Adam Rooney to fire home the second before half time.
The best Inverness could muster was a half chance for Nick Ross and an Adam Rooney effort that Andy Graham cleared.
Caley Thistle new boy Adam Rooney was impressive after he came on at half-time, but he could not find an equaliser.
Foran's rising strike then fizzed over before Kilmarnock goalkeeper Cammy Bell made a fine stop to keep out an Adam Rooney shot from 12 yards.
Adam Rooney came on at half-time for Russell Duncan, while Imrie and Cowie switched flanks, as home boss Craig Brewster looked to get Inverness back on level terms.
Samaras and striker partner Gary Hooper had quiet games against Inverness, with midfielder Joe Ledley grabbing both goals after Inverness had gone in front through an Adam Rooney penalty.
Meanwhile, Butcher was hopeful that top scorer Adam Rooney, the subject of a failed bid from Russian club Kuban Krasnodar, would remain at Caledonian Stadium beyond the end of January.
It was Grant Munro who headed in from a Richie Foran delivery to seal the victory, while Adam Rooney had fired the visitors ahead from the penalty spot, only to see Andrius Velicka equalise.
Rooney's team-mate Adam Watene died in October 2008 after suffering a massive heart attack while training in a city centre gym.
Wayne Rooney edged United ahead with a spot kick three minutes later only for Adam Le Fondre to restore parity in the 19th minute.
Adam Johnson, who excelled as a substitute for Theo Walcott after he was stretchered off with an ankle injury following Rooney's goal, added an expertly taken second after 69 minutes to confirm his growing maturity on the international stage.
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