Hopes of an overall majority were all but dashed when the ultra-marginal seat of Dumbarton – held by Scottish Labour’s Jackie Baillie – refused to budge and remained coloured red.
There is still a pathway to an overall majority for the SNP, but it requires an unlikely set of results, including gaining Aberdeenshire West and at least one regional list seat in the Highlands and Islands.
The result will likely intensify demands for indyref2 with a pro-independence majority secured with the combination of the SNP and the Scottish Greens.
But Prime Minister Boris Johnson said his impression was Scottish voters had “moved away from the idea of a referendum”.
“I don’t think this is anything like the time to have more constitutional wrangling, to be talking about ripping our country apart, when actually people want to heal our economy and bounce forward together,” he told a national newspaper. “That’s what people want.”
Alba, led by Alex Salmond, is set to fail to gain seats. The former first minister told The Scotsman he may not stand for party leader after the election.
With 48 constituency results declared on Friday, the SNP had 39 seats, Liberal Democrats four, Conservatives three and Labour two.
Ms Sturgeon, who won her seat in Glasgow Southside with 60 per cent of the vote, told reporters: “My focus, if we are re-elected as the government, is to get back to work to steer the country through the crisis and into recovery.
“That remains the case. But once the crisis is over, and if there is a majority in the parliament for an independence referendum, people should have the right to choose our future. Scotland’s future should always be in Scotland’s hands.”
Speaking about the prospect of winning an overall majority, the SNP leader added: “It’s certainly not impossible, but nor is it guaranteed.
“That was always going to be on a knife edge. It comes down to a small number of votes in a small number of seats, so at this midway point it is certainly still there as a possibility, but I have never taken that for granted.
“It is a long shot, to say the least, in a PR system. To win a majority, you effectively have to break the system. I would like to do it, but I have never been complacent about that.”
Results came in fits and starts during the day with key ministers in Ms Sturgeon’s Cabinet after the election re-elected one by one.
Deputy first minister John Swinney, justice secretary Humza Yousaf and finance secretary Kate Forbes all easily held on to their seats which were never in doubt.
Other government ministers – economy minister Fiona Hyslop, higher education minister Richard Lochhead and tourism minister Fergus Ewing – were all returned as was housing minister Kevin Stewart.
However, the SNP’s most notable gains of the day in Ayr and East Lothian may come at the expense of minister for energy Paul Wheelhouse, who will now have to sweat out the results of the regional list in the hopes of returning to Holyrood.
In a day where most of the seats failed to change hands, the SNP victory in Ayr – where Siobhian Brown narrowly beat incumbent since 2000 John Scott by just 170 votes – was their narrowest of the day.
In East Lothian, the seat of retiring former Scottish Labour leader Iain Gray was snatched away from Anas Sarwar’s party by SNP candidate Paul McLennan.
Holyrood will also see the return of one of the SNP’s most recognisable figures in Angus Robertson who swept away the challenge from the Scottish Conservatives in winning Edinburgh Central.
The seat – famously won unexpectedly by Ruth Davidson in 2016 during the Scottish Conservative renaissance – was not even close as the former Moray MP won with a majority of almost 5,000.
Dumbarton, however, was where realistic hopes of an outright SNP majority were dashed.
Ms Baillie, one of the few remaining members of the class of 1999, continued her record of winning what was the most marginal seat in Scotland, beating challenger Toni Guigliano by just under 1,500 votes.
The fate of Scottish Tories leader Douglas Ross on the list is likely to be positive given the SNP’s success in the Highlands and Islands and the Scottish Greens were confident of returning both Patrick Harvie and Lorna Slater as co-leaders to Holyrood.
Anas Sarwar was defeated in his constituency battle with the First Minister, but will be all but guaranteed a seat via the regional list and said his party had injected a bit of energy into the campaign.
The Scottish Labour leader’s ultimate test will be on the regional list, but he said he was honest about the scale of the challenge facing his party.
He said: “The process of changing is not complete, we have got to carry that on.
"We've got a project and a plan and we’re going on a journey to build a credible alternative and that journey continues.”
Mr Sarwar added that he was disappointed by the loss in East Lothian, but pointed to overall progress since he was elected leader when Scottish Labour sat at 14 per cent in the opinion polls.
He said: “Even my biggest critics can see that over the course of the last ten weeks we've got the Labour Party back on the pitch.
"I think people can see that I'm a different kind of leader, trying to build a different kind of party, and together rebuild a different kind of country."
Scottish Liberal Democrat leader Willie Rennie emphatically held on to his seat in North East Fife.
Speaking after holding onto his seat, Mr Rennie said: “I hope all the candidates in this election hear the message from the voters that now is not the moment for another referendum.
“We need to listen to that.”
Douglas Ross, the Scottish Tory leader, said there had been a “mixed picture” across Scotland, with surges in Tory support in some areas, but disappointing results in others.
Later in the day Scottish Liberal Democrat Alex Cole-Hamilton become the big winner from pro-unionist tactical voting, easily beating the SNP’s Sarah Masson in the marginal of Edinburgh Western with more than 25,000 votes.
This pattern was repeated in Eastwood where former Scottish Conservative leader Jackson Carlaw was returned to Holyrood thanks to pro-union voters and Edinburgh Southern gave Daniel Johnson a renewed mandate as a Scottish Labour MSP.
The failure to win those seats may prove crucial, with the SNP now relying on positive results in Aberdeenshire West, currently held by the Conservatives, and at least one list seat in the Highlands and Islands.
Achieving all of that would still only see the SNP win a majority should it lose no other seats set to be announced on Saturday.
For Mr Salmond, the day was chastising.
Early results from the regional list votes suggest the former first minister is likely to be heading for electoral oblivion, with estimates that his new party Alba is barely registering 2 per cent nationwide.
When asked by the BBC if he believed his party would make the breakthrough, the former first minister said: “I don’t think so, on the results we've seen.”
He went on to blame his party’s apparent failure to make any meaningful gains on the BBC’s decision to exclude Alba from the debates, but added the party’s argument around “wasted” SNP votes on the regional list had “proven to be correct”.
Mr Salmond said: “I think probably we will take out of this election the arguments we have been putting forward will be proven to be correct. Firstly, that independence should be front and centre of election campaigns if we want to persuade people to vote for it.
“Crucially, it seems perhaps a million, perhaps even more than a million, SNP votes on the regional list are going to elect perhaps one, perhaps two MSPs on that section of the ballot paper across Scotland. What a waste.”
Success for the opposition parties will come down to the regional list with both the Conservatives and Labour vying for second place overall.
Results are expected to be announced from around 6pm on Saturday evening, with a final result likely by the end of Saturday evening.