Needing 60 votes to pass, it was approved 68 to 29 with bipartisan support.
At the same time, the White House issued a veto threat against a House Republicans' bill introduced this week that would provide $622 million, a figure the White House called "woefully inadequate" to fight the rapidly spreading virus that can cause serious birth defects in newborns.
"The administration's full request of $1.9 billion is needed to reduce the risk of the Zika virus, particularly in pregnant women, by better controlling the mosquitoes that spread Zika; develop new tools, including vaccines and better diagnostics to protect the Nation from the Zika virus; and conduct crucial research projects needed to better understand the impacts of the Zika virus on infants and children," the White House said in a statement.
Republicans initially resisted providing new funds for Zika, arguing leftover money from the recent Ebola outbreak should be used first. But Democrats pressured their counterparts daily, arguing the GOP was ignoring a dire public health crisis that would grow worse as the mosquito-borne virus spread north from South America during the summer months.
After weeks of negotiations, Republican Missouri Sen. Roy Blunt and Democratic Sen. Patty Murray of Washington agreed to the $1.1 billion in emergency funding.
Blunt insisted to reporters Tuesday the U.S. response has not been negatively impacted by the time it took to reach a deal because federal agencies have been cleared to spend Ebola funds on Zika.
"No harm is done here. The Congress is taking this seriously. I would hope that in a matter of a few weeks we'll reach a final conclusion and that conclusion will allow all of the agencies involved to plan their Zika spending up to the end of next fall," Blunt said.
Even White House spokesman Josh Earnest acknowledged the Senate bill was "making more progress" than the one in the House.
The House on Wednesday is scheduled to vote on its bill, which is expected to pass with mostly Republican votes.
There are two points of contention with the House that will need to be resolved. One deals with the overall funding level. The second deals with whether to offset the costs, a perennial battle between the parties that has halted progress on less urgent bills in the past. But in this case, with so many Senate Republicans agreeing not to seek offsets, pressure will be on House Republicans to act, especially in an election year.
The proposal that passed the Senate was one of three measures the Senate voted on Tuesday. It rejected a plan from the two senators from Florida, Democrat Bill Nelson and Republican Marco Rubio, that would have granted Obama's full request. Needing 60 votes, it failed 50 to 47.
Another proposal from Senate Republican Whip John Cornyn would have provided cost offsets for the $1.1 billion. That measure failed 52 to 45.