Goalkeeper Jamie Langfield made a successful comeback as Aberdeen profited from two Inverness own goals on a miserable afternoon for the hosts.
Langfield - making his first appearance for almost a year - made a string of good saves in the first half.
Roman Golobart headed a long-throw into his own net in the 46th minute.
And Kenny Gillet saw the ball strike him and rebound into the net after Jonny Tuffey had saved from Josh Magennis in the final minute.
Langfield, who was playing his first competitive game in 11 months after recovering from a brain seizure, palmed away an early Gregory Tade drive.
The Dons keeper parried again moments later when Jonny Hayes tested him with a low drive but Inverness struggled to fashion clear-cut opportunities for the rest of a drab encounter.
Steve Williams had the ball in the net in the 38th minute but his effort was ruled out for offside.
Aberdeen, despite lacking a cutting edge, took the lead moments after the break when Magennis's long throw-in was headed by Golobart but his attempted clearance found the net.
Inverness failed to capitalise on their lionshare of possession and Shane Sutherland spurned a great chance to equalise seven minutes from time when he blazed over.
And the Dons made Terry Butcher's side pay when they doubled their lead in the closing stages with another own goal.
Magennis ran through on goal and his shot was blocked by Tuffey's feet and the rebound bounced off French defender Gillet into the net.
The second own goal compounded Inverness's misery and consigned them to a ninth home defeat of the season.
Inverness manager Terry Butcher:
"We dominated periods of possession and looked a threat, although we didn't create any clear-cut chances - more half chances than anything else.
"We've not done enough to win the game and that's disappointing.
"The fans were booing us at the end and quite rightly. If I had of paid to watch that then I would have done exactly the same."
Aberdeen manager Craig Brown:
"I think you have to compliment both sides because we each had eight players under the age of 21.
"I've seen better games of football and we were fortunate to score through two own goals.
"However, it gave us the chance to bring 16-year-old Cammy Smith on, which was great, while Fraser Fyvie is learning and improving all the time.
"I know Inverness had three suspended, but we had nine out injured at what is a very difficult place to come to, so it was pleasing to get the result, especially with so many young players on the pitch."
Goal! - Kenny Gillet - Inverness 0 - 2 Aberdeen Kenny Gillet concedes an own goal. Inverness CT 0-2 Aberdeen.
Jamie Langfield takes the direct free kick.
Substitution Johnny Hayes leaves the field to be replaced by David Proctor.
Chris Clark fouled by Owain Tudur Jones, the ref awards a free kick.
Free kick awarded for an unfair challenge on Aaron Doran by Fraser Fyvie. Direct free kick taken by Aaron Doran.
Effort on goal by Josh Magennis from just inside the area clears the bar.
Unfair challenge on Owain Tudur Jones by Russell Anderson results in a free kick. Strike comes in from Johnny Hayes from the free kick.
Effort on goal by Shane Sutherland from just inside the penalty area goes harmlessly over the target.
Free kick taken by Andrew Considine.
Booking The referee books Richie Foran for dissent.
The assistant referee flags for offside against Richie Foran.
Free kick awarded for a foul by Steve Williams on Josh Magennis. Direct free kick taken by Andrew Considine.
Andrew Considine concedes a free kick for a foul on Richie Foran. The ball is crossed by Aaron Doran, Steve Williams has a headed effort from close range and clears the bar.
The official flags Cameron Smith offside. Jonny Tuffey takes the free kick.
Substitution Chris Clark on for Ryan Jack.
Foul by Russell Anderson on Johnny Hayes, free kick awarded. Strike on goal comes in from Aaron Doran from the free kick.
Inswinging corner taken right-footed by Aaron Doran, Owain Tudur Jones challenges Andrew Considine unfairly and gives away a free kick. Jamie Langfield restarts play with the free kick.
Shot by Johnny Hayes from just outside the area goes over the net.
Corner taken by Aaron Doran, clearance made by Andrew Considine.
Corner taken by Johnny Hayes from the left by-line, clearance made by Andrew Considine.
Josh Meekings fouled by Josh Magennis, the ref awards a free kick. Free kick taken by Johnny Hayes.
Andrew Considine takes the free kick.
Substitution Rory McArdle on for Mitchel Megginson.
Josh Meekings challenges Mitchel Megginson unfairly and gives away a free kick.
Kenny Gillet concedes a free kick for a foul on Josh Magennis. Free kick crossed right-footed by Ryan Jack.
Foul by Johnny Hayes on Andrew Considine, free kick awarded. Direct free kick taken by Andrew Considine.
Substitution Nick Ross joins the action as a substitute, replacing Gregory Tade.
The referee blows for offside. Direct free kick taken by Jonny Tuffey.
Substitution Billy McKay goes off and Shane Sutherland comes on.
Direct free kick taken by Johnny Hayes. Effort on goal by Steve Williams from just inside the box goes harmlessly over the target.
Booking Josh Magennis is cautioned.
Free kick awarded for a foul by Josh Magennis on Gregory Tade.
Free kick awarded for an unfair challenge on Josh Meekings by Mitchel Megginson. Direct free kick taken by Steve Williams.
Substitution Cameron Smith on for Rory Fallon.
Shot from just outside the box by Ryan Jack goes over the bar.
45:47 Goal scored
Goal! - Roman Golobart - Inverness 0 - 1 Aberdeen Own goal by Roman Golobart. Inverness CT 0-1 Aberdeen.
The second half has started.
45:00 +0:12 Half time
Half Time The match has reached half-time.
Gregory Tade concedes a free kick for a foul on Gavin Rae. Jamie Langfield takes the free kick.
The assistant referee flags for offside against Steve Williams. Free kick taken by Jamie Langfield.
Johnny Hayes crosses the ball from the free kick left-footed from right wing, Gavin Rae makes a clearance.
Booking The referee cautions Andrew Considine for unsporting behaviour.
Foul by Andrew Considine on Johnny Hayes, free kick awarded.
Aaron Doran fires a strike on goal direct from the free kick, save by Jamie Langfield.
Booking Ryan Jack is shown a yellow card.
Free kick awarded for a foul by Ryan Jack on Kenny Gillet.
Free kick awarded for a foul by Mark Reynolds on Richie Foran. Owain Tudur Jones restarts play with the free kick.
Owain Tudur Jones challenges Mitchel Megginson unfairly and gives away a free kick. Russell Anderson takes the direct free kick.
The official flags Billy McKay offside. Free kick taken by Jamie Langfield.
Free kick awarded for an unfair challenge on Steve Williams by Mitchel Megginson. Jonny Tuffey takes the free kick.
Owain Tudur Jones concedes a free kick for a foul on Fraser Fyvie. Ryan Jack takes the free kick. Kari Arnason takes a shot. Blocked by Richie Foran.
Unfair challenge on Fraser Fyvie by Josh Meekings results in a free kick. Andrew Considine takes the direct free kick.
Free kick awarded for an unfair challenge on Richie Foran by Gavin Rae. Richie Foran restarts play with the free kick. Aaron Doran produces a right-footed effort from long distance that goes harmlessly over the bar.
The referee penalises Billy McKay for handball. Kari Arnason takes the direct free kick.
Unfair challenge on Mitchel Megginson by Josh Meekings results in a free kick. Andrew Considine restarts play with the free kick.
Fraser Fyvie is caught offside. Free kick taken by Jonny Tuffey.
Billy McKay is ruled offside. Free kick taken by Russell Anderson.
Mitchel Megginson takes a inswinging corner. Handball decision goes against Josh Magennis. Jonny Tuffey takes the free kick.
Steve Williams concedes a free kick for a foul on Rory Fallon. Gavin Rae takes the direct free kick.
Andrew Considine has an effort at goal from outside the penalty box missing to the wide right of the goal.
The referee blows for offside against Billy McKay. Free kick taken by Jamie Langfield.
Rory Fallon concedes a free kick for a foul on Roman Golobart. Direct free kick taken by Kenny Gillet.
Aaron Doran takes a shot. Comfortable save by Jamie Langfield.
Free kick awarded for an unfair challenge on Richie Foran by Andrew Considine. Free kick taken by Jonny Tuffey.
Johnny Hayes has an effort at goal from 20 yards. Save made by Jamie Langfield.
The referee blows for offside. Indirect free kick taken by Jamie Langfield.
Mitchel Megginson is ruled offside. Indirect free kick taken by Jonny Tuffey.
Gregory Tade takes a shot. Jamie Langfield makes a save.
Free kick awarded for a foul by Josh Magennis on Aaron Doran. Free kick taken by Kenny Gillet.
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