Following a goalless first half at the Caledonian Stadium, Spanish defender Roman Golobart headed into his own net 48 seconds after the restart.
Full-back Kenny Gillet doubled the lead with a minute to go when Josh Magennis' shot rebounded off goalkeeper Jonny Tuffey on to the Frenchman and across the line.
Aberdeen, who only mustered the one shot on target throughout the game, leapfrogged Kilmarnock who are not playing until tomorrow.
Aberdeen goalkeeper Jamie Langfield was among six changes to the line-up who went down 2-1 against Hibernian in last weekend's Scottish Cup semi-final.
The shotstopper, who had not played a competitive game for 11 months, replaced Jason Brown.
Fraser Fyvie, Josh Magennis, Mitchell Megginson, Russell Anderson and Gavin Rae came in for Rory McArdle, Chris Clark, Clark Robertson, Stephen Hughes and Scott Vernon.
Caley Thistle's suspended trio of Greg Tansey, Graeme Shinnie and Ross Tokely were the only alterations to the side who drew 0-0 at St Johnstone two weeks ago.
Inverness brought back top scorer Gregory Tade, on-loan defender Steve Williams and winger Aaron Doran, who made his first appearance since January.
The hosts started positively with Tade threatening early when his low volley from the edge of the area was blocked well by Langfield.
The keeper parried again moments later when Jonny Hayes fired low after good work from Doran.
Langfield's busy period continued when he thwarted Doran's effort from range on the quarter hour.
The Dons rallied and Andrew Considine shot just wide with their best chance of the opening stages.
Doran might have opened the scoring in spectacular fashion midway through the half but his 20-yard curler landed on the roof of the net.
The Irishman was on target with a 25-yard free-kick just after the half hour but Langfield was equal to it.
Williams had the ball in the net after 39 minutes for Inverness, yet the celebrations were shortlived as it was ruled out for offside.
Aberdeen could have snatched an advantage on the stroke of half-time when Ryan Jack fired low inches past the post after being played in by Rae.
The game sparked back to life 48 seconds after the restart when Golobart netted his third own goal of the season to put Aberdeen ahead.
Magennis' long throw-in was headed towards goal by the Spanish defender and although Inverness keeper Jonny Tuffey got a hand to it, he could not stop it crossing the line.
It was the on-loan Wigan centre-back's second own goal in Aberdeen's favour after he scored for them in a 2-1 win for Inverness on Christmas Eve.
Williams sent a free-kick on the edge of the box over the crossbar on the hour as the hosts tried to find an equaliser.
The Inverness pressure continued to mount as Owain Tudur Jones directed a header just wide from a Josh Meekings throw-in.
Aberdeen absorbed the pressure and hit back when Fyvie ran to the byline before laying the ball off to Rae, whose thunderbolt was blocked by a sprawling Golobart.
Visiting fans called for a penalty but their pleas were waved away by referee Steven Maclean.
It was a brief interlude as Inverness continued to search for a leveller with Doran putting a 25-yard free-kick just over.
Williams connected with another Doran free-kick moments later but failed to direct it on target.
On-loan Bradford defender Williams then found Richie Foran, who played in substitute Shane Sutherland who blazed over with seven minutes to go.
Aberdeen capitalised on the squandered chances by doubling their lead after 89 minutes when Gillet scored an own goal.
Magennis ran through on goal and shot low from eight yards straight at Tuffey's feet and the rebound bounced off French defender Gillet into the net.
It compounded Caley Thistle's misery as the home side fell to their ninth home defeat of the season.