The Lib Dem leader was also forced to admit that he could not force one of his most senior ministers, Business Secretary Vince Cable, to vote with him and back the Coalition's economic strategy.
Mr Clegg told the party conference at the Scottish Exhibition and Conference Centre (SECC) in Glasgow he was not running a "boot camp"
The leadership argued that it had to stick with its fiscal mandate or risk allowing the Conservatives to claim all the credit from the emerging economic recovery.
But Mr Cable has warned in recent days that that recovery is weak and could be derailed if plans to help homebuyers obtain mortgages trigger a new housing bubble.
In the end, however, and despite earlier suggestions that he would not even attend the debate, Mr Cable voted with the leadership as its motion was carried. Aides to the minister described the split with the leadership as a "storm in a teacup". But last night Mr Cable defended his stance, saying it was his "duty" to speak out.
Earlier, delegates had made pleas for the party to abandon what they condemned as "Osbornomics".
They said the party had to set clear blue water between its policies on the economy and those of the Tories before they entered into the next general election.
To applause from the floor of the conference hall one Lib Dem member, Naomi Smith, said: "We must not vote for an ideological merger with the Conservatives".
Another delegate called for the party not to go into the next election on the "coat tails of George Osborne ."
"If we are not going to distinguish ourselves from the Tories the question what are the Lib Dems for is quite a valid question," she added.
Gareth Epps, from Reading, suggested that if the leadership motion prevailed the party could go into the next election marching toward the sound of gunfire. "I want the ammunition in order to fight that battle and win," he told the conference.
Earlier delegates were warned by Steve Webb, the pensions minister, that abandoning the Coalition's economic policies risked handing the Tories all the credit for the recovery.
In a separate debate the leadership narrowly defeated a call for the reinstatement of the 50p rate, by a margin of just four votes.
Critics claim the abolition of the higher rate, a key Conservative policy, has given a tax cut to millionaires.
Mr Cable later claimed that he had always intended to vote in the economy debate.
Earlier this week, Mr Clegg rejected the Business Secretary's call for limitations on the government scheme, Help to Buy, which is designed to help many more people get a mortgage.
Mr Cable said he was "not apologetic" about his comments on the economy.
"Maybe people do think I am a bit blunt. I do not regard that as a criticism."
He added: "Where there are differences in our coalition I am perfectly willing to fire off about it. There has been this flurry about the housing market. I thought that someone in Government had to say something. I said it.
"Maybe it's ruffled a few feathers. I'm not apologetic."
Mr Cable insisted he was "on the same page" as Mr Clegg on economic issues, and coalition differences on the recovery were down to "emphasis".