After the First Minister and Prime Minister sealed months of negotiations by signing the Edinburgh Agreement, Mr Salmond refused to confirm that guidance from the Electoral Commission on the question to be put on ballot papers and the poll's ground rules would be followed.
The body has been handed a central role in advising on contentious issues, including the wording of the question voters will face, plus spending limits for the main campaign organisations and political parties.
But the First Minister stressed the SNP-dominated Scottish Parliament would have the final say.
He said: "The Government proposes, the Electoral Commission advises and the Parliament decides.
"That's the process that pertains for Westminster and Scottish elections and it's the process the Electoral Commission have set out themselves."
On the wording of the question, Mr Salmond said the Government would also take into account the outcome of its own consultation, in addition to testing of the single question carried out by the commission.
He added: "Both of those things will inform the Parliament's decision when it comes."
His refusal to give a cast-iron guarantee over the Commission's verdict sparked alarm among his opponents.
Labour's deputy leader Anas Sarwar said: "We must let the Electoral Commission make these decisions. Let's take them out of the hands of politicians.
"What we can't have is Alex Salmond wanting to be a player and the referee.
"We must respect a neutral arbiter to come up with the right question and the right ground rules and abide by that.
"We can't have this process gerrymandered."
Scottish Secretary Michael Moore, who negotiated the agreement with Deputy First Minister Nicola Sturgeon, said: "In the past, successive UK Governments have followed the recommendations of the Electoral Commission on campaign finance and other issues.
"I think the expectation is that's what would happen here."
Answering questions from MPs, Scotland Office Minister David Mundell told the House of Commons: "It's very difficult to envisage circumstances in which the Scottish Government would want to ignore the commission's recommendations.
"No Government has ever ignored those recommendations previously.
"There would be not just a procedural issue but a significant political price to pay for any party that sought to do so."
When Mr Sarwar suggested the First Minister and his colleagues were already "rowing back" from the commission's role, Mr Mundell replied: "I don't agree with him that Mr Salmond or the Scottish Parliament can blithely ignore the recommendations.
"It would be a serious political matter if that were to happen."
The Commission is due to test the Government's preferred wording: "Do you agree that Scotland should be an independent country", which has faced criticism from some MPs who claim it is biased.
The watchdog's call for a £1.5 million limit on the Yes Scotland and Better Together campaigns has already fallen fall of the Scottish Government, who want it capped at half that.
John McCormick, the Electoral Commissioner for Scotland, said: "We will play our full part in ensuring that voters can have confidence in the result.
"In March this year we set out our principles for how the referendum should be run and we will assess any detailed proposals against these principles as they are brought forward."
The row threatened to overshadow a historic day for the Scottish Government, whose plan to hold the referendum in the autumn of 2014 is now legally watertight.
The Edinburgh Agreement, signed at the Scottish Government's St Andrew's House headquarters by the First Minister, Prime Minister, Deputy First Minister and Scottish Secretary, will transfer legal powers enabling Holyrood to hold a single question referendum by the end of 2014.
The SNP Government will be able to give 16 and 17-year-olds the vote, as it promised, though a mechanism for registering the teenagers has yet to be announced.
Mr Salmond said the decision to rule out a second question on so-called "devo max", which he wanted the option of posing, was a compromise worth making to ensure that the referendum result was respected.
He said the deal was a "significant step in Scotland's home rule journey" and insisted the Yes campaign would go on to win the vote, despite starting 25 points behind in the polls.
He said: "Just as I've believed in independence all my life I believe that with all my soul."
David Cameron, who also paid a symbolic visit to Rosyth in Fife, where the Royal Navy's largest ever warship is being built, said: "I passionately believe in the United Kingdom. I think the rest of the United Kingdom, England, Wales, Northern Ireland, is better off with Scotland in the United Kingdom.
"Mine will be just one voice of many saying we are better together, let's stay together."
Mr Moore predicted a win for the pro-UK campaign, adding: "Game on. I believe we'll get a strong endorsement of Scotland remaining part of the UK."
Iain McMillan, director of CBI Scotland, said: "We argued strongly that the referendum should be legally watertight and offer one question only about whether or not Scotland should become independent. That has been achieved today.
"We would have preferred the referendum to take place sooner than the autumn of 2014 in order to remove the undoubted uncertainties for business that are arising from this lengthy process.
"But we accept the current timetable will provide for a thorough exploration of the issues"
Johann Lamont, Scottish Labour leader, said: "We are pleased that we have finally reached an agreement that should allow Scotland to have a fair and decisive referendum."
Patrick Harvie, co-convener of the Scottish Greens, said: "This deal signals the start of the real debate, and a yes vote in October 2014 would signal the start of a new Scotland."
However, Willie Sullivan, Scottish director of the Electoral Reform Society, said: "We now have a deal that suits the interests of a few dozen people in Edinburgh and Westminster and excludes a large section of the Scottish people who want more powers within the UK."
