The amendment to a highway funding bill failed 51-47, The Washington Post reported. The House approved the extension last week.
"The Republicans are coming forward with another attack on federal workers," Sen. Benjamin L. Cardin, D-Md., said during a brief debate.
Sen. Pat Roberts, R-Kan., sponsored the amendment. It would have used the savings from the pay freeze to finance a tax credit for adoption, tax deductions for college and property taxes and energy projects.
The last across-the-board raise for federal employees was 2 percent in January 2010. The Obama administration has proposed a .5 percent increase in January 2013.
Sen. Barbara Mikulski, D-Md., said public employees should not be "treated as scapegoats."
"They are already operating under a pay freeze, they are already facing deep cuts at their agencies, yet they continue to be targeted by Republican plans to extend their pay freeze or pass backdoor pay and benefit cut," she added.