Although 11 Democrats joined Republicans in supporting the plan, the vote fell four votes short of the 60 required for approval of the controversial pipeline that would move oil recovered from tar sands projects in Alberta, Canada, to southern U.S. refineries.
Supporters say the pipeline will create jobs and reduce U.S. dependence on oil from volatile countries, while opponents say the pipeline is an environmental hazard and there's no guarantee the oil, a particularly dirty crude oil, will end up in U.S. gas pumps.
Obama rejected a bid in January to expedite the pipeline, saying Congress didn't provide enough time to review the risks.
The White House said Obama Thursday lobbied Democrats to block passage of the amendment.
"He made some calls," press secretary Jay Carney told reporters. "The president believes that it is wrong to play politics with a pipeline project whose (exact) route has yet to be proposed."
Senate Republicans slammed Obama for his lobbying efforts, CNN said.
Senate Minority Leader Mitch McConnell, R-Ky., accused Obama of trying to block "the biggest private-sector job-creation project in our country."
"At a moment when millions are out of work, gas prices are literally skyrocketing and the Middle East is in turmoil, we've got a president who is up making phone calls trying to block a pipeline here at home. It's really almost unbelievable," McConnell said Thursday during his opening remarks on the Senate floor.
Critics question the proposed job numbers for the project, and environmental groups are concerned about the impacts of both the pipeline and the tar sands oil, which is the dirtiest type of crude oil.