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Angus Robertson, the SNP’s former Westminster leader, won Central from the Tories with a majority of nearly 5,000 and is now expected to be handed a key job in Nicola Sturgeon’s government.
But Labour’s Daniel Johnson saw off the SNP challenge in Edinburgh Southern with a majority of 4,022 over nationalist Catriona MacDonald.
And in Edinburgh Western, Alex Cole-Hamilton held the seat, winning more than half the total votes and a majority of 9,885 over SNP candidate Sarah Masson.
His success was hailed as a “landslide” by one supporter.
The results mean the Tories no longer hold any constituencies in Lothian, although the indications are they have done well on the regional list.
The Capital’s remaining three constituencies – Edinburgh Eastern, Edinburgh Northern & Leith and Edinburgh Pentlands – will count on Saturday and Lothian’s seven list seats will be allocated once all the results are known.
Tactical voting is seen as having played a key role in helping Labour and the Lib Dems retain Edinburgh Southern and Edinburgh Western.
The Conservatives and Lib Dems urged supporters to use their constituency votes to back the candidate most likely to stop the SNP.
It looks as if that paid off well in allowing two of Edinburgh’s six seats to remain in opposition hands, though it did not work so well in Central.
Turnout was up significantly in all of the three Capital seats counting on Friday.
Mr Johnson interpreted his victory as an endorsement of the agenda set by new Labour leader Anas Sarwar.
He said he had been given an “unequivocal” mandate by the people of Edinburgh Southern to focus on what united people and not to reopen the wounds of the past.
"They are clear I must work relentlessly to pursue recovery and must reject decisively a second divisive independence referendum,” he said.
And Mr Cole-Hamilton’s huge win in Edinburgh Western came along with a big fall in the Tory vote and despite the SNP getting their biggest vote in the seat.
He said: "We had been pretty confident for a couple of weeks that it wasn't going to be close and we were not just getting tactical votes, but a sense of people feeling well-served by my five years in parliament and for me that's the most rewarding aspect of it."
In Central, where Ruth Davidson took the Tories from fourth place to win last time with a narrow majority of 610, it may have been less clear for potential tactical voters to accept the Conservatives were the ones to back.
The seat had been held by Labour for three terms before being won by the SNP in 2011.
Mr Robertson said his election was “unequivocally a vote that I should support a fourth-term SNP Scottish Government with Nicola Sturgeon as First Minister and that we should have a say, all of us, about Scotland’s future. As democrats we should not fear that.
"The circumstances have changed with the Brexit vote. Edinburgh is the most pro-European part of the country and I think the people want to have their say as to us being able to find a way back to the European Union.
"It will come and I’m sure people in Edinburgh will vote Yes.”