Billy McKay's penalty just before the hour ultimately proved enough to earn three points for Caley Thistle after Paul Lawson had cancelled out Andrew Shinnie's early opener.
The home side made the brighter start as McKay's smart turn and shot was palmed wide by Michael Fraser, but he was beaten in the fifth minute when he failed to hold onto Richie Foran's header and Shinnie tapped in the rebound.
Torrential rain hampered the quality of the action as chances came at a premium, but Lawson served up a moment of class on 35 minutes as his magnificent strike from 30 yards beat Ryan Esson and found the top corner.
Esson limped off moments later with a suspected groin injury after Grant Munro's bullet header shaved the woodwork, and Shinnie had a shot deflected wide after the break before Iain Vigurs' volley was narrowly off target at the other end.
But Inverness restored their lead on 59 minutes when McKay slammed in his 24th goal of the season from the spot after Mihael Kovacevic was adjudged to have hauled down Charlie Taylor.
Sam Morrow had a shot charged down and then saw a decent header in added time well claimed by Esson's replacement Antonio Reguero as Thistle held out to move within three points of second-placed Motherwell.