Shadow chancellor John McDonnell said the "real people's vote" would be a general election.
Mr Corbyn was speaking as a poll found 86pc of Labour members think voters should have the final say on the outcome of Brexit negotiations, and 90pc would now vote to remain in the EU.
Ever since the United Kingdom voted in 2016 to leave the EU, Labour has said it will respect the result - but it wants a closer relationship with the bloc than the one that Prime Minister Theresa May's Conservative government is seeking.
The weakened support for a People's Vote is despite polls showing overwhelming support within the party membership for a referendum on the final deal, and thousands turning out over the weekend to march for a final say outside the party's conference.
A caller lost his temper with the Labour front bench for "changing their stance" on Brexit and the idea of a second referendum.
He told the Sunday Mirror newspaper "I'm not calling for a second referendum".
In a hint that the option of remaining in the European Union might not be on the table in any future referendum, he said the form of the question would be decided by Parliament but "it will be about whether you accept the deal or not, or whether you send people back to negotiate a proper deal".
More than 100 local Labour associations have submitted motions to the conference urging a public plebiscite, with a choice between leaving on terms agreed upon by the government or staying in the EU.
A crowd waving European Union and other flags chanted "bollocks to Brexit" and "it's not a done deal" as they walked from St George's Hall to a rally at Pier Head, close to where the conference is taking place.
But counter-protester Les Thomas, a self-described socialist, highlighted Corbyn's quandary, saying "the working class people I know, they've joined the Labour party but are firmly in the Brexit camp".
To cheers he highlighted that people from across the United Kingdom were present, saying: "They are saying squarely to the leadership of the Labour Party "listen to us, hear us, give us a People's Vote".
With Theresa May reeling after European Union leaders rejected her Brexit plans, it is the first conference that party leader Jeremy Corbyn can see a realistic route to becoming prime minister. I hope we will agree that the best way of resolving this is a general election.
However, after a mammoth five-hour debate of party members and union delegates, Labour has made a decision to ask its members to back a complex motion which fails to rule out either a General Election or a new referendum.
"That could trigger a General Election and we're ready for it".
Mr Lammy warned that Labour needed to fight against the likes of prominent Brexiteers Boris Johnson, Jacob Rees-Mogg and Nigel Farage who, he said, have the "radical right standing behind them".
The scandal has deepened the divisions between Corbyn's far-left supporters and the more centrist faction of MPs who held power in the party after Tony Blair took charge in 1994. "They know where their members are and they know where their voters are".
"There was a wide range of views shared and discussed, with people expressing different opinions on the matter of a further referendum".
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