Lawmakers say they hope the issue will be resolved later this month as part of a bipartisan spending package.
The 52-46 vote came as Florida health officials announced seven more locally transmitted cases of Zika.
Florida has now reported 56 locally transmitted cases of Zika, which is often spread by mosquitoes.
Florida officials have called on lawmakers to release funds to help fight the spread of the disease, which is linked to severe birth defects in pregnant women.
The Republican-backed Senate bill included a provision that would have prevented Planned Parenthood in Puerto Rico from receiving new funding to fight the spread of the Zika virus, which can be s**ually transmitted.
Senate Minority Leader Harry Reid, a Democrat from Nevada, said Republicans were “more interested in attacking Planned Parenthood” than “protecting women and babies from this awful virus”.
Democrats blocked similar funding measures in June and July before Congress left for the summer recess.
Before the vote, Republican Senate Majority Leader Mitch McConnell blamed his Democratic counterparts: “It’s hard to explain why, despite their own calls for funding, Democrats would block plans to keep women and babes safe from Zika.”
Republican House Speaker Paul Ryan has indicated that lawmakers will work to include funding for Zika in a budget deal or a continuing resolution that Congress must pass to avoid a government shutdown at the end of September.
The Centers for Disease Control and Prevention (CDC) announced that it had spent nearly all of the $22 million allocated to the agency in the fight against Zika.
As of late August, there were more than 2,700 cases in United States and more than 14,000 in US territories, most of which were reported in Puerto Rico.
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