Labour, backed by other opposition parties, led a rare motion of no confidence at Holyrood one week after raising concerns about the handling of a decision to reverse proposals to shut acute mental health beds in North Lanarkshire.
But Mr Neil was able to rely on the SNP's majority and two independent MSPs to ensure the attempt failed in a 57-67 vote.
"This is just trumped up by the Labour Party, total nonsense from beginning to end, and I'm getting on with the day job of looking after the health service in Scotland," he said after the decision in Parliament.
"If they want to play petty politics, that's entirely up to them. We're getting on with the serious business of governing Scotland."
The row, which dominated business in Parliament, was sparked last week when Labour revealed emails detailing Mr Neil's actions after taking over from Nicola Sturgeon at the end of 2012.
The party says he overruled widely supported plans for mental health services shortly after taking over the health brief.
Only after the intervention did Mr Neil tell Parliament he would step back from the issue to avoid any perception of a conflict of interest, Labour argues.
Johann Lamont, the Scottish Labour leader, demanded answers during First Minister's Questions - for the second week in a row.
"Let's look at what I believe is his charge sheet," she said.
"Putting his political interest before patients - guilty. Undermining the integrity of health professionals - guilty. And misleading this Parliament and the people of Scotland."
Just 30 minutes later, her colleague Neil Findlay led the formal motion of no confidence.
"The dogs in the street know what Alex Neil has been up to," he said.
"He has been caught holding the smoking gun and the First Minister and his deputy know it.
"We believe he has misled his constituents, we believe he has misled this Parliament."
Mr Salmond said the decision - affecting Monklands Hospital in Airdrie - was good for people served by NHS Lanarkshire.
"This is about health provision in Lanarkshire that affects 500,000 people and the Health Secretary was well within his rights to look at health provision in Lanarkshire, the particular proposals that were coming forward, and make his views known," he said.
Public health minister Michael Matheson said there was no conflict of interest because the issue went wider than Mr Neil's Airdrie and Shotts constituency.
But Labour maintains that no credible reason has been given for why the best option, signed off by Ms Sturgeon, was replaced by the "worst option" available.
Mr Matheson said: "The facts are straightforward. Alex Neil made his view known, he weighed up all the options and the opinions. He did so without fear or favour.
"If Labour wish to argue against that decision, that's their right. But that's not what they're doing.
"They're throwing everything they can at the man. Their objective is not about the quality of services provided in Lanarkshire, this is about getting at the Health Secretary."
He questioned the reason to pick this row for a motion of no confidence.
"It's the first that I can think of that any health secretary has been attacked for not closing a hospital ward," he said.
"It's the first time that a health secretary has been attacked for saving part of our NHS.
"But then, there is no scare story too silly for the Labour Party, no smear too low for the Labour Party, and no accusation too base that they would not seek to use against this SNP Government. That's what we're seeing today."
But demands for Mr Neil's dismissal continued.
Labour MSP Dr Richard Simpson said there was a clear failure to separate personal interest as an MSP from the role of minister.
"It was, I regret to say, an abuse of power, compounded by misinforming Parliament, continued involvement, and the prevention of the release of emails which had to have an information commissioner to release them," he said.
"He, therefore, must see his position is untenable. He must do the decent thing now and resign."
Tory MSP John Lamont said: "This whole episode is symptomatic of the SNP's disregard for this Parliament, particularly in the run-up to the referendum.
"It gives us no pleasure to conclude that in this instance the Cabinet Secretary deliberately ensured that Parliament was misled.
"By having clearly done so, we can no longer have confidence in his duties, and so we support the motion of no confidence."
The Liberal Democrat group and Greens also sided with Labour.
It is only the third motion of no confidence since the Scottish Parliament was established in 1999.
In December 2000, the SNP questioned the role of Labour MSP Sam Galbraith, who was education minister during a school exams fiasco.
A second motion, in February 2001, questioned Labour transport minister Sarah Boyack for awarding trunk roads contracts to private firms.
Both attempts failed when put to the vote.