The close vote in the House, which a week earlier rejected a related bill, kept alive Obama's goal of bolstering US ties with Asia through the 12-nation Trans-Pacific Partnership agreement, the economic element of a foreign policy shift aimed in part at countering the rising influence of China.
The TPP would encompass 40 percent of the global economy.
But the outlook in the Senate for fast-track, seen by Japan as crucial to sealing the deal on TPP, was uncertain.
Senate aides said support among Democrats hinged on another trade issue, the Export-Import Bank, which may have to close at month's end.
The House's vote was its second in less than a week on fast-track, which would restrict lawmakers to a yes-or-no vote on trade deals. Democrats last week blocked it by voting down a companion measure to extend aid for workers hurt by trade.
That was a slap in the face to Obama, who urged his fellow Democrats to support fast-track and the worker assistance program, despite skepticism among Democrats close to labor unions about the impact of trade deals on US jobs.
In an unusual alliance, the president and Republican House Speaker John Boehner turned last Friday's loss into a win by excising the worker aid program that was voted down by the House. That neutralized the ability of some Democrats' to use it to stymie fast-track, and capitalized on support from a bloc of 28 pro-trade Democrats.
Those House Democrats resisted intense pressure from unions, after House and Senate Republicans - who generally oppose the worker support program - promised to attach the worker assistance bill to a separate trade bill.
SENATE BACK IN FOCUS
The trade package still faces three more congressional votes, including two in the Senate, which took nearly two weeks in May to approve fast-track and worker aid.
"The House took the hot potato and threw it back to the Senate," said Lori Wallach of consumer group Public Citizen, which was campaigning against fast-track.
Many Democrats feared trade deals such as the TPP would cost US jobs as employers chase lower costs in signatory countries.
Republicans, who generally favor trade, would not have the muscle to pass fast-track on their own, especially in the Senate, where a super-majority is needed for major legislation.
Senate leaders plan to include the worker aid program in a bill renewing trade benefits for African countries, with a vote possible next week, but the plan is not stitched up yet.
Democratic Senator Ron Wyden said that pro-trade Democrats were determined to pass both fast-track and the worker aid program.
"We're having almost around-the-clock meetings to make sure the process is such that it actually will happen," he said.
Senator Heidi Heitkamp, one of 14 Democrats who backed fast-track in May, said she was waiting to see the path forward for the worker program and a customs bill - and a vote on the Export-Import Bank, known as Ex-Im.
Some Republicans wanted to close down Ex-Im, which provides support to US exporters and buyers of US goods. Its charter expires at the end of the month. Republicans promised a vote as part of a deal to pass the trade package on its first run through the Senate.
"I'd love to see this as an opportunity to do something to avoid the charter for the Ex-Im Bank to expire," Heitkamp said.
The House vote was a positive sign for the TPP, which was sold as harmonising standards on issues such as intellectual property and labor protections, and lowering trade barriers among the dozen emerging and developed countries.
The deal, backed by the business community, would open new markets for major U.S. exporters such as Boeing, General Electric, Ford, IBM, Caterpillar, Merck and Cisco, policy analysts said.
Negotiators were under pressure to finish the pact, which is already more than five years in the making, to allow the TPP to clear the US congress before the 2016 US presidential election campaigns began to dominate the agenda.
Some TPP partner countries want fast track in place before making final offers on the trade deal, which economists estimate would boost the global economy by almost $300 billion a year.