The home side had the first chance of the match as Graeme Shinnie tried to power the ball in from outside the box, but saw his effort saved.
Craig Reid tried to lob the ball in from 25 yards out for the visitors, but the strike was just tipped over, preventing Motherwell from taking the lead.
Iain Vigurs had a chance to double Motherwell's lead shortly after the restart, but Inverness soon started to dominate as they tried to find an equaliser.
Motherwell's defence kept the home side out of their penalty area for much of the second half, but Inverness were able to get back on level terms when Ryan Christie drilled the ball in low from just outside the box.
Shinnie came close to adding a late winner for the home side, but his attempt to tap in from a corner was stopped, and allowed Craig Moore to catch the Inverness defence out on the counter-attack, setting up Vigurs for Motherwell's second.