The six, who include Scottish leader Lord Christopher Monckton and chair Mike Scott-Hayward, stood down as ballot papers were about to be sent out.
But the party pushed ahead with the selection and David Coburn, who is Ukip's London chair, was the controversial winner. A party source described the process as a "shambles" and evidence of London "parachuting in" a candidate.
Ukip in Scotland has failed to replicate the party's success south of the Border, where Farage and his team have elected representatives in town halls and Brussels. At recent Holyrood by-elections, Otto Inglis polled 4.83% in Aberdeen Donside and Peter Adams got 3.75% in Dunfermline.
But Ukip in England is tipped to do well in next year's European election, with the Scottish party in the hunt to take one of Scotland's six MEP seats.
The prospect of a breakthrough prompted some of the Scottish wing's biggest hitters to stand in the contest.
Nine candidates were shortlisted: Monckton; Scott-Hayward; Inglis; Coburn; Paul Henke; Ross Durance; Malcolm Macaskill; Steven McKeane; and Kevin Newton.
The selection was aimed at whittling down the nine hopefuls to six.
Whoever came top of the internal ballot had, in the words of one insider, a "decent" chance of becoming an MEP next year. But the selection has prompted an extraordinary bout of infighting and a civil war between the UK party and its Scottish branch. On the eve of ballot papers being sent out to Scottish members in September, some candidates became concerned about the alleged tactics being used by Inglis.
There was also suspicion about the presence in the race of Coburn, who was believed to be an ally of Farage.
Fears were aggravated when Ukip's Lanarkshire branch sent an email saying it endorsed Coburn and Inglis as "preferred lead and second candidates". The statement added: "Lanarkshire branch office bearers and members are thereby requested to canvass and cast votes on behalf of David Coburn and Otto Inglis alone."
The grievances came to a head at a candidates' summit in Edinburgh in September. Seven of the nine - the exceptions being Inglis and Coburn - resigned as candidates in an email to Ukip chair Steve Crowther. They stated: "We withdraw as candidates for European parliamentary seats."
In a clear dig at Coburn, they claimed that "Ukip's leader had invited a London friend to stand", adding a senior figure in the contest had "unfairly advantaged him".
The letter complained about the alleged tactics of another candidate, which a source confirmed as Inglis.
They said of the Lanarkshire email: "A branch broke the rules by widely endorsing these two candidates."
The candidates claimed that Ukip in London "twice refused" to suspend the ballot pending an investigation.
It is understood Newton reversed his decision to quit.
Despite this meltdown, Ukip sent ballot papers to Scottish members with all nine candidates on it.
With more than half of the contenders no longer competing, it left the relatively unknown Coburn with a huge opportunity, which he took, as he topped the poll.
One source said Ukip has presided over a "shambles" in Scotland: "It would appear they think parachuting in a London-based Scot is the answer. You cannot invite candidates to join a fair election fight when in reality the whole ballot appears to have been fixed from the start."
The source added: "We have blown any prospects of electoral success in next year's European elections."
Ukip recently published the results of the list rankings for Wales, Northern Ireland and regions in England, but not Scotland.
Coburn describes himself as "Lead Ukip Scotland MEP Candidate" on his Twitter feed.
The mass resignation is the latest setback for Farage's party in Scotland. Earlier this year, Farage had to abandon a press conference in an Edinburgh pub after being heckled.
He said: "The anger, the hatred, the shouting, the snarling, the swearing was all linked in to a desire for the Union Jack to be burnt."
Asked about the resignations, Lord Monckton said: "I just want to confirm where we've got to with London. Once that's been sorted out, the position will become clear."
Asked why he resigned, he said: "We will go into all of that after London has come up with its answer."
Henke said of his decision to withdraw: "It was about fairness. I took my name off the list."
Inglis said: "Speak to someone further up the tree."
Coburn said that he had won the internal contest, but denied Farage had asked him to stand. Asked about the six resignations, he said: "I can't really discuss the list. I'm just a candidate like everyone else."
He added: "There is no civil war in Ukip Scotland. There are always disgruntled people everywhere."
Macaskill, Durance and Scott-Hayward did not return calls.
McKeane declined to comment, while Newton could not be contacted.
SNP MEP Alyn Smith said: "Ukip in Scotland are clearly in turmoil, and the reality is that people are not buying the prejudice they are selling."
A Ukip spokesman said: "Ukip's candidate list for the European Elections in Scotland has not yet been announced because of a dispute within Ukip Scotland, which has seen some candidates, including the Scottish Leader Lord Monckton, at odds with others.
"Several of the candidates, including Lord Monckton, withdrew from the list in September shortly before the ballot papers were despatched. The Party's National Executive Committee decided that it would nonetheless proceed with the ballot, which was won by David Coburn.
"The NEC has subsequently reviewed the situation and, with the withdrawn candidates declining its requests to return to the list, has resolved to move forward.
"David Coburn will be the lead candidate, supported by a full list of nationally approved candidates which will be announced shortly."