In a pair of votes, Democrats blocked taking up GOP bills to pay for a public health response to the virus and to fund the Pentagon next year leaving in doubt Congress' ability to pass either bill.
Each failed to get the 60 votes needed to advance.
If an agreement is not reached, the government could shut down on September 30, just a few weeks before the presidential and congressional elections. However, several congressional Republicans suggested the Zika and government funding issues would be combined and resolved together ahead of the deadline.
"It's hard to explain why -- despite their own calls for funding -- Senate Democrats decided to block a bill that could help keep pregnant women and babies safer from Zika," Senate Majority Leader Mitch McConnell said on the floor. "It's also hard to explain why -- despite the array of terror attacks we've seen across the world -- Senate Democrats decided to block a bill that could help keep the American people safer from threats like ISIL."
The Zika vote came as the mosquito-borne virus, which can also be transmitted sexually, spreads widely in the Puerto Rico and some US states. Democrats blocked the bill because they say it included a provision to prevent funding for Planned Parenthood and no longer included a provision in the House bill banning Confederate flags from veterans' cemeteries.
"Republicans were more interested in attacking Planned Parenthood and flying the Confederate flag -- can't make this stuff up, that's really the truth -- than protecting women and babies from this awful virus," Senate Minority Leader Harry Reid said.
The raw politics of the standoff -- and the blunt language used by the two leaders -- speak to the maneuvering and positioning McConnell and Reid see as necessary as they fight for control of the Senate, which is be up for grabs this year. Republicans hold a narrow 54-46 advantage but have several vulnerable senators who could lose in November.
Reid applies pressure
In a related move Tuesday, Reid said Democrats would work to increase pressure on Republicans to confirm Merrick Garland to the Supreme Court. Garland's nomination has floundered for months because Republicans say they want the next president to make that life-long appointment.
Reid said until the Judiciary Committee schedules confirmation hearings for the judge, Democrats would use the chamber's rules to hold up action in Senate committees.
"To show the Americans' disgust with how the Republicans have treated Merrick Garland's nomination, we're objecting to the committees meeting," Reid said.
Senate rules require all senators to agree for committees to meet for more than two hours after the Senate convenes. It was put in place originally to ensure senators don't stray for too long from their duties on the floor. Typically, extending that time is done with little fanfare or notice.
It's not clear what the long-term practical impact will be, although there are several hearings Wednesday that might need to be canceled.
An Aging Committee hearing is planning to examine the Bipartisan Policy Centers recommendations to boost retirements savings. A Veterans Committee hearing is looking at "best practices" at the Veterans Health Administration. And the Foreign Relations Committee is examining the Comprehensive Nuclear Test Ban Treaty.
Reid said he was open to allowing some hearings if there are "extraordinary circumstances" and McConnell requests it.
Republicans predicted Reid's plan will backfire because it's just as inconvenient for Democrats as it is for Republicans.
"Every time he surprises me he comes back and outdoes himself and surprises me again," said Sen. John Cornyn, the second-ranking Republican who is from Texas. "I just think that's an unsustainable position."