Video report by ITV News Correspondent Paul Brand
Jeremy Corbyn has seen off an attempt to commit the party to a confirmatory referendum on any Brexit deal.
The proposal was defeated in a marathon meeting of the party's ruling National Executive Committee (NEC) to finalise the Labour platform for next month's European elections.
There had been calls for the party to offer a second referendum in all circumstances from MPs - including deputy leader Tom Watson - and unions.
However, the manifesto agreed upon by 66% of votes is broadly the same as Labour's autumn conference pledge: that it will back a second referendum only if a general election and a Labour deal cannot be delivered.
Party leader Mr Corbyn had come under pressure to shift Labour's stance on a second vote as the ruling National Executive Committee (NEC) met on Tuesday to finalise its manifesto.
ITV News Political Correspondent Paul Brand says "yet again" Labour has decided to "keep all the options open", and despite the lack of pledge to back a second referendum whatever the Brexit deal is, those seeking a public vote say they are happy that at least one is mentioned in the manifesto.
Some 115 MPs and MEPs had signed a letter to NEC members organised by the Love Socialism, Hate Brexit group urging them to explicitly back a referendum in the manifesto.
The change was backed by a number of major unions, including the GMB, Unison and Usdaw.
And 34 of Labour's 70 candidates in the May 23 European elections have pledged to campaign for a referendum and then back Remain if a vote is called.
Members of the party on both sides of the argument played down expectations of fireworks and the 41-member NEC, which brings together representatives of the party leadership, MPs and members as well as unions, described the meeting as "respectful, constructive and comradely throughout".
However, deputy leader Tom Watson, who has led calls for a more positive stance on a second referendum, left the six-hour meeting without comment, saying only that the manifesto would be published early next week.
Mr Watson had earlier walked out of a shadow cabinet meeting after being told it would not be shown the proposed wording of the manifesto commitment.
Mr Corbyn did not speak to waiting reporters as he arrived by a side entrance and left the same way.
The outcome of the vote came just hours after Labour's Jess Phillips warned Labour will be on the end of a "drubbing" in the European elections if the party does not offer a second referendum.
Speaking on ITV News' podcast, Acting Prime Minister, the Birmingham Yardley MP said: "I think people who voted Remain and voted Labour will not vote Labour again.
"I do think we'll get a drubbing in the European elections. All the main parties are going to get a drubbing in the European elections."
Stop Brexit protester Meg Gain from Stratford upon Avon said she was one of five activists to block Jeremy Corbyn's car as he and shadow home secretary Diane Abbott left the NEC meeting.
"We just stood in front of the car and shouted we wanted to stand up for the 80% of Labour voters who want to remain in the EU," Ms Gain said.
"He didn't say anything to us, he just walked in front of us and got straight in the car.
"We stood in front of the car just for a few minutes.
"As far as I'm concerned they have lost my vote completely because they're just not an opposition."
A Labour spokesperson said the party is the only one "which represents both people who supported Leave and Remain.
"We are working to bring the country together after the chaos and crisis created by the Tories."
Ahead of the meeting Mr Watson headed told ITV News: "People are telling on the doorstep... is this has been a Parliamentary failure and so like them I've come to the conclusion that we need to ask the people to decide on the deal.
"It seems obvious to me that [European election] candidates are telling us they want a confirmatory ballot on any deal that Parliament can decide and I'm sure we'll have that discussion in the meeting today."
The meeting came as cross-party talks aiming to break the impasse continue, with the de facto deputy prime minister David Lidington describing discussions on Monday as “positive” and “productive”.
It is understood the Government is hoping a conclusion may be reached towards the middle of next week.
Mrs May has set out two possible outcomes from the cross-party talks - a compromise deal to get the Withdrawal Agreement through Parliament or a series of indicative votes in the Commons backed by both major parties.
It remains unclear whether the parties will be able to bridge the gap between them on issues such as a future customs union in the coming days, but any resolution next week would almost certainly come too late to prevent European elections going ahead.
However, Foreign Secretary Jeremy Hunt said questions remained as to whether Labour was "serious about delivering Brexit".
The EU’s chief Brexit negotiator Michel Barnier said on Monday he hoped to see results this week from the talks and reiterated a call to “fix Brexit quickly”.