Caley dominated long spells of the game and created a host of chances, but they took until the 89th minute to seal the game when sub Aaron Doran added to Greg Tansey's first-half strike.
Motherwell were on the back foot early on and Ross Draper went close to opening the scoring in the sixth minute, his header going narrowly wide of Dan Twardzik’s goal.
Motherwell were almost gifted the lead however after quarter of an hour, Inverness captain Graeme Shinnie selling goalkeeper Dean Brill short with a pass-back meaning he could only find the feet of Lionel Ainsworth with a scuffed clearance.
The winger's attempted lob looked bound for the net all the way only for Gary Warren to get back in the nick of time to clear off the line with his head.
Tansey brought out a save from Twardzik with a good effort from 25 yards, but the Motherwell 'keeper could only push the ball wide where Marley Watkins whipped in a cross that Billy McKay somehow failed to convert from close range.
Only a fantastic block by young debutant David Ferguson prevented Ryan Christie from slotting home after a ball across the face of goal from Watkins but John Hughes' men finally got the goal their play deserved after 42 minutes.
Tansey picked the ball up in midfield and drifted forward unchallenged before picking his spot with a great finish into Twardzik's bottom right-hand corner.
Stuart McCall reacted to his side's poor first-half showing by replacing the ineffectual Ainsworth with Henrik Ojamaa at the break - Ojamaa's first appearance since his midweek loan move from Legia Warsaw.
But it was still Inverness who out-worked and out-played 'Well and, apart from one break by Stuart Carswell down the right when the midfielder did well to flash a ball across goal, the visitors were rarely threatened.
There was little more goalmouth action to speak of but that suited the visitors, who were content enough to sit on their lead and eventually confirm victory a minute from the end of the 90 minutes.
Doran raced down the left before cutting inside and bending a beautiful right-foot finish beyond Twardzik, the final score not flattering the visitors at all.