Opponents of independence said that the vote meant that there was “confusion” over whether a welfare cap would be introduced in an independent Scotland.
The row came as MPs overwelmingly backed the UK government’s new cap on welfare in a historic vote which will mean benefit payments cannot exceed £119.5 billion next year.
The cap in welfare spending set by Tory Chancellor George Osborne in George Osborne was agreed to by Labour leader Ed Miliband but condemned by some in his party as “short term political posturing”.
The measure, in the Charter for Budget Responsibility, comfortably passed the Commons 520 to 22, majority 498, with 13 Labour rebels joining the Scottish National Party, Plaid Cymru and Green MP Caroline Lucas opposing it.
During the debate, SNP Banff and Buchan MP Dr Eilidh Whiteford warned that the “pernicious measure” would play in the independence referendum underlining the UK’s record for inequality.
She said: “The cap once again puts the most disadvantaged people in our communities on the front line. It is blatant ring-wing politics, not aimed at solving any of the long term problems which are getting worse because of Westminster’s austerity agenda, an agenda now supported by all the anti-independence parties.”
But pro-UK politicians said that the SNP position was confiused.
In August last year Mr Salmond said: “If you have the right cap deployed in the right way, then that is a reasonable thing to have.”
Scottish Conservative welfare spokesman Alex Johnstone MSP said: “The SNP are absolutely clueless when it comes to welfare issues.
“They showed their real colours by voting against a measure that will help to bring the welfare bill under control.”
Labour shadow Scotland Office minister, Russell Brown said: “The SNP are completely confused about how they would keep welfare spending under control. Last year, Alex Salmond said that he could support a welfare cap, but today his MPs voted against it.”
Detailing his plans, which were unveiled in last week’s Budget, Chancellor George Osborne said: “This is about building a welfare system that is fair to those who need the system and fair to people who pay for the welfare system.
“It was not fair benefits were unlimited, we have introduced a cap. It wasn’t fair those looking for work faced marginal tax rates as high as 96 per cent, sapping the incentives to find a job. We are addressing that through universal credit.”
The welfare cap includes all benefits except the state pension and jobseekers allowance.