Irish duo Jonny Hayes and Adam Rooney were both on target to seal maximum points against the Dons in their ninth SPL meeting at Tulloch Caledonian Stadium and give Terry Butcher's men back-to-back league wins for the first time this season.
And the Dons ended the game with 10 men as substitute Michael Paton was shown a straight red card in the 66th minute for a foul on Hayes.
Hayes set Caley Thistle on their way when he netted the opening goal with a cross-come-shot after 18 minutes.
And Rooney made it two when he took advantage of a mix up between Zander Diamond and Mark Howard to chip home the second.
Dons manager Mark McGhee made three changes to the starting line-up which lost 3-2 to Rangers at Pittodrie last Sunday.
In a surprise move goalkeeper Jamie Langfield was replaced by Howard because McGhee thought the he could distribute the ball better in windy conditions.
A hamstring injury picked up in training ruled out Nikola Vujadinovic, while Chris Maguire missed out due to suspension.
It opened up the opportunity for Ryan Jack to make his debut, while Josh Magennis also came in.
Butcher made one change to the side which beat St Mirren 2-1 in Paisley last time out with Nick Ross replacing the injured David Proctor.
It could have all been different if Aberdeen had not been denied the opening goal after only two minutes but referee Calum Murray spotted a foul in the Inverness penalty area.
Derek Young floated a dangerous free-kick into the area for Dons captain Zander Diamond to power home a header from close range but the celebrations for the visitors were cut short by Murray who penalised Diamond for climbing on Ross Tokely.
The Dons maintained their pressure with Scott Vernon guiding a header inches wide after connecting with a Darren Mackie cross.
Eric Odhiambo looked to be ready to pull the trigger after latching onto a good through ball from Hayes but Jerel Ifil made the saving tackle.
Aberdeen's Mackie forced the first real save of the game when his shot from outside the box was parried clear by Ryan Esson.
In an end-to-end battle Hayes flashed a shot wide from the edge of the box after being picked out by Russell Duncan moments before opening the scoring.
The diminutive midfielder's effort from the right-wing floated over goalkeeper Howard and into the net.
Aberdeen's pursuit of an equaliser led to a scrappy passage of play fought out in midfield with neither side creating any further chances in the first half.
Rooney squandered a chance to increase Inverness's advantage two minutes after the interval when he was played through by Hayes.
He beat Jerel Ifil to go one-on-one with goalkeeper Howard, but last season's top scorer for Inverness uncharacteristically steered his shot just wide of the post.
Dons substitute Mitch Megginson almost had an immediate impact when his cross from the left was header inches wide by Darren Mackie.
Aberdeen debutant Ryan Jack forced a save with a header from another Megginson cross, before Rooney scored on the counter attack in 61 minutes.
Diamond tried an audacious clearance which Rooney pounced on before chipping an onrushing Howard.
Aberdeen were reduced to 10 men when substitute Paton was sent off for a straight red card.
The Dons attacker had only been on the pitch for 16 minutes before he was dismissed for fouling Hayes.
Substitute Mitch Megginson was also on the pitch for around 16 minutes before he was taken off the pitch on a stretcher following a challenge from Tokely, for which the Inverness defender was booked.
Aberdeen almost grabbed a consolation in the closing stages but Darren Mackie prodded his shot wide.
Despite six minutes of stoppage time, Aberdeen failed to prevent Inverness recording their first win against the Granite City side since August 2008.