A tense clash in the Highlands was decided by a Richard Offiong strike on the stroke of half-time.
Hamilton came into the game as league leaders and underdogs, but left Tulloch Caledonian Stadium with maximum points after the first league meeting of these sides.
The last time the sides met, Inverness cruised to a 6-1 Scottish Cup fourth round win, but not today.
Caley Thistle's newest signing, striker Adam Rooney, came off the bench to provide the fans with some cheer.
But the Republic of Ireland Under-21 international, who completed a £50,000 move from English Premiership Stoke City on Friday, failed to repeat the form which he produced for Inverness on a pre-season tour of Denmark when he was on trial at the SPL club.
Another SPL debutant was 19-year-old centre back Jamie Duff, who replaced club captain Grant Munro, who was ruled out with a knee injury picked up in ICT's 2-0 win at Aberdeen last weekend.
Caley Thistle started brightly with Roy McBain warming the hands of Hamilton keeper Tomas Cerny in the opening minutes. The midfielder sent a stinging angled volley goal-bound after an Andrew Barrowman flick-on.
The home side were almost gifted the lead at the mid-point of the half when Ian Black played through Don Cowie, whose cross was headed inches wide of his own goal by defender Chris Swailes.
Cowie himself came close on the 32 minutes, but his header from a Duff cross was off the mark.
Hamilton had their first chance three minutes later when a Tony Stevenson corner was headed on by Simon Mensing for Offiong to nod over the crossbar.
An edge of the box free-kick broke up the visitors' dominance, but Cowie could only direct it high of the goals.
In stoppage time Offiong outmuscled the inexperienced Duff before running 20 yards, shrugging off Russell Duncan, before slotting the ball calmly past Michael Fraser into the bottom corner.
The addition of Rooney at half-time added a spark to Caley Thistle's crowd which transcended onto the pitch briefly when a good run from the 20-year-old ended with Cowie having another chance thwarted.
Attacks were at a premium despite Rooney making it a two-pronged attack alongside Barrowman failed to bear fruit, however, and was later switched to three up front when Rory McAllister came on in the closing stages.
Teenage striker Lucas Akins came on to replace Offiong in 57 minutes and the ex-Huddersfield Town hitman also caused problems.