The bill -- which was put into final form in negotiations between House and Senate Republicans but not Democrats -- fell eight votes short of the 60 it needed to advance. Congress now has just a narrow window to find a compromise before departing Washington in mid-July for a lengthy recess.
Senate Majority Leader Mitch McConnell, R-Kentucky, said it was "absurd" Democrats filibustered the bill and said he hoped they would feel pressure as they explained to their constituents this weekend why they voted against the money.
McConnell said he would schedule a vote on the bill again next week.
Democrats said they opposed provisions blocking funds for Planned Parenthood and freezing some environmental regulations to allow for spraying of the mosquitoes that carry the virus. They accused Republicans of inserting those "poison pills" to secure the backing of far-right Republicans in the House at the expense of being able to pass it in the Senate.
Top Democrats sent a letter to GOP leaders seeking fresh negotiations on the bill. While McConnell appeared wary of new talks, others GOP senators, like Roy Blunt of Missouri, who has been heavily involved in the issue, acknowledged they would be necessary.
"We have to deal with this. Everybody understands that this has to be dealt with," Blunt said.
Republicans argued that they had met the funding level acceptable to Senate Democrats and charged that Democrats backed off the bill because of pressure from special interests, like Planned Parenthood.
"This is purely and simply about politics on the part of the Democrats. And worse yet, special interest politics that has gotten in the way of what's in the best interest of the safety and health of the American people," said Sen. John Thune, R-South Dakota.
The rhetorical attacks were surprisingly harsh -- even for this divided Congress -- as each side blasted the other's handling of the issue as motivated more by base politics than the health care needs of women who if infected with Zika can have children with serious birth defects.
"Republicans decided they'd leverage a national health emergency and a public health crisis to sneak in special interest poison pills," said Sen. Chuck Schumer, D-New York.
"It is completely unacceptable, actually shameful, hypocritical, cynical for the Democrats to block this funding at this time," said Sen. John Cornyn, R-Texas, who earlier gave a lengthy floor speech while standing next to a blown up photo of a baby with a shrunken head due to microcephaly, the birth defect linked to Zika.
"We all realize what a threat this is to the public health and safety of women in the United States," he said.