Senators voted 39-60 on the Massachusetts Democrat's amendment, which would have prevented "fast-track" procedures from being used on deals that included Investor-State Dispute Settlements (ISDS), which allow foreign companies to challenge U.S. laws.

Under fast-track, the president can get trade deals approved by Congress through a simple majority vote and lawmakers are blocked from changing the agreement.

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"This amendment protects America's sovereignty and the rule of law," she said ahead of the vote.

Warren's amendment split Democrats, with Sen. Ron Wyden (D-Ore.) asking senators to vote "no" and suggesting ahead of the vote that Warren was trying to combat a problem that didn't exist.

"We have never lost an investment dispute case and never paid a dime in penalties. Here's our record: 17 cases, 17 victories," Wyden said.

The amendment likely would have undermined the ongoing talks with 11 Asia-Pacific nations. Obama defended ISDS's to reporters earlier this year, saying it can't "undo" American laws.

"They don’t have the ability to result in punitive damages. ISDS has come under some legitimate criticism when they’re poorly written," he said.

It's the second time Warren has been blocked on trade this week.

Sen. Orrin Hatch (R-Utah) blocked her unanimous consent request earlier this week to pass legislation that would require President Obama to make the details of a trade agreement public before senators decided whether or not to grand it fast-track status.