John McDonnell joined the Government to vote down a Labour backbench proposal to protect the customs union on Monday.
Joined by 18 fellow Labour MPs, the shadow chancellor voted with 283 Conservatives, eight DUP and two independents to defeat an amendment to the Taxation Bill pushed by Labour MP Ian Murray.
MPs heard the Bill, which will place into law a new post-brexit customs regime, would allow the UK to charge customs duty on goods, including those imported from the EU.
Murray's amendment sought to exempt EU goods from the new regime, a move supported by Tory rebels Anna Soubry and Ken Clarke.
However, speaking ahead of the vote, shadow Treasury minister Anneliese Dodds said the proposal could "worsen our situation," albeit unintentionally.
Murray said in response: "If she [Dodds] disagrees with the technical aspects of my amendment, but agrees with the principle of staying in the customs union, where are the frontbench amendments to do that?"
Dodds said Labour wanted to "keep all options on the table", adding: "Ultimately we are seeking to have a more democratic process, we aren't able to vote on that which is unfortunate.
"I think he will know that ultimately, as I stated before, the Labour position is to leave all options on the table and that is the best thing for Britain to be doing.
"It is very, very unfortunate that the Government side have failed to do that because it is enormously damaging for our negotiating position.
"I very much regret that the Government still could irresponsibly and recklessly lead us to a no deal scenario and in that case these amendments sadly would worsen our situation, I know that is not intended by the proposers, quite the opposite.
"I'm afraid that is what technically they would lead to."
Murray's amendment was defeated by 311 votes to 76, majority 235.
Alongside McDonnell and Dodds, Shadow International Trade Secretary Barry Gardiner and shadow Treasury colleagues Peter Dowd and Jonathan Reynolds also voted against the amendment.
Speaking during a pre-vote debate on the customs union, former minister Soubry said: "It can't be right that the overwhelming majority of honourable and right honourable members in this place agree that we should be in the customs union and the single market.
"And the only reason that that isn't even on the table anymore, and it's an uncomfortable truth, is because I fear my party is in hock to 30 to 35 hard, ideologically driven Brexiteers."
Writing on Twitter after the vote, Gardiner called amendment "illiterate" as he explained why he voted against it.
"We voted against an amendment that would have taken away any safety net against a no deal Brexit,” he wrote.
"Under WTO (World Trade Organisation) rules UK would have been unable to impose any tariff on goods from any country in the world. Amendment was illiterate."