Candidate Angus MacDonald gained a majority of 2,160 over the SNP’s Drew Hendry.
The SNP candidate had already conceded defeat after a recount delayed the result.
It means the Liberal Democrats have won 72 Westminster seats, six of which are in Scotland, meaning they have overtaken the Scottish Conservatives.
The outcome had originally been expected at about 05:00 on Friday, but there was a recount – then candidates were told the votes would need to be counted again on Saturday morning.
Returning officer Derek Brown said the delay was due to a discrepancy between the verified votes total and the provisional number of counted votes.
Local businessman Angus MacDonald was elected after he received 18,159 votes, while the SNP candidate was second with 15,999 votes.
Former MP Mr Hendry had already conceded defeat to his Lib Dem rival.
In a statement on Friday evening he said it had been “an absolute joy” to serve the people of Inverness, Nairn, Badenoch and Strathspey for the last nine years – and that he was disappointed not to be continuing as an MP for Inverness, Skye and West Ross-shire boundary.
The seat is new under boundary changes, made up of the previous Ross, Skye and Lochaber and Inverness and Nairn, Badenoch and Strathspey constituencies.
These seats were both held by the SNP.
Ian Blackford who was MP for Ross, Skye and Lochaber and Inverness announced before the election he would not stand for re-election.
All other constituency results were announced on Friday.
The Liberal Democrats now have six seats in Scotland, making them the third biggest party in the country in terms of MPs.
Labour won a landslide victory in Scotland with 37 seats – a gain of 36.
The SNP, who won 48 seats in 2019, have been reduced to nine, while the Scottish Conservatives have five seats, down one from their previous total.
Speaking after his election, Mr MacDonald said: “The Highlands has been left behind of decision-making moving to Holyrood and Westminster.
“I hope that I can become an important part in reversing this and play a key role in delivering substantial infrastructure and improvements to our constituency.”
He added that his party wants to move “power and budgets” back to communities.
This is a really meaningful victory for the Lib Dems.
There has been a deeply-held resentment about how the SNP treated former Lib Dem leader Charles Kennedy and the tactics used to unseat him before his death.
To win back this seat, albeit with new boundaries, is a poignant moment for them.
The count took place in the same location at the Highland Football Academy in Dingwall where the former Liberal Democrat leader used the phrase “the night of the long sgian dubhs “ to describe the SNP’s astonishing victory in almost every Scottish seat in 2015.
As one activist put it: “It’s an exceptionally special day for many of us, as we return something taken.”
‘We blew the doors off it’
The leader of the Scottish Liberal Democrats, Alex Cole-Hamilton, said winning the seat, in an area once held by Lib Dem stalwart Charles Kennedy, was the “icing on the cake” to a successful election for his party.
Speaking on BBC Radio’s Good Morning Scotland, he said: “We targeted our resources on the seats we were most likely to win and we outperformed absolutely all of our expectations.
“We got absolutely everything we targeted and not just by a fraction, we blew the doors off it.”
The party is now the third biggest in the House of Commons, with 72 Liberal Democrat MPs being elected.
Mr Cole-Hamilton said this would give his party “tremendous momentum” heading into the 2026 Scottish Parliament elections.
“We’re a bigger seat at the table and with that comes an audience with the people of Scotland which I think we have earned now.
“People will start to hear what we have to offer and it will be positive and it will be focused on the issues that matter to them,” he said.
