The vote was 53-43. Democrats had criticized Bernhardt, saying he continued to advise a California water district even after he withdrew his formal registration as a lobbyist last year.
Republicans called Bernhardt a capable lawyer with vast experience on issues important to the West, including endangered species, water use and development of public lands. Bernhardt was Interior's top lawyer in the George W. Bush administration.
A spokeswoman said Zinke was "excited to have David Bernhardt, a highly-qualified, veteran official, return to the department to help advance 'America First' policy priorities" set by Trump.
Sen. Maria Cantwell, D-Wash., said Bernhardt's nomination flies in the face of Trump's pledge to "drain the swamp" in Washington of influence peddlers.
"I'm afraid he's not draining the swamp. He's actually helping to fill it," Cantwell said.
The League of Conservation Voters and other environmental and watchdog groups urged senators to oppose Bernhardt's nomination, saying he has long lobbied for the oil and gas industry, mining companies and other businesses regulated by Interior.
"Bernhardt's list of conflicts of interest is extensive and should disqualify him from this position," 150 groups said in a letter to senators.
"Strongly worded press releases issued by special interest groups alleging any wrongdoing are patently false and are desperate attempts to stop the progress that is being made at the department on behalf of the American people," said Heather Swift, a spokeswoman for Zinke.
Sen. Lisa Murkowski, R-Alaska, said she thinks Bernhardt "will be a very capable second-in-command to Secretary Zinke, helping to steer the department in a positive direction."
But Cantwell and other critics said they were concerned over media reports that Bernhardt was working for the Westlands Water District, the nation's largest irrigation district, at the same time he was serving on the Trump transition team. Bernhardt's law firm represented Westlands in four lawsuits against Interior.
At a confirmation hearing in May, Bernhardt told Cantwell he would recuse himself from matters involving Westlands and other clients for at least a year, unless he receives authorization to do so.
"If I get a whiff of something coming my way that involves a client or former client for my firm, I'm going to ... run straight to the ethics office," Bernhardt said.
Cantwell was unimpressed. "I remain concerned about his record on behalf of these corporations at the expense of the environment, his tenure at the Department of the Interior and many other challenges," she said.
Sen. Bill Nelson, D-Fla., said he opposed Bernhardt because of his refusal to support a moratorium on oil drilling off the Florida coast in the eastern Gulf of Mexico.
"When it comes to the eastern Gulf, there is no good way to increase offshore production while balancing environmental concerns," Nelson said, noting that the 2010 BP oil spill fouled the gulf region for years.
Nelson helped pass a congressional ban on oil drilling 125 miles off Florida's coast more than a decade ago. The ban is set to expire in 2022 and a number of congressional Republicans and industry groups are in favor of ending it.
Trump signed an executive order in April to expand oil drilling in the Arctic and Atlantic oceans, reversing restrictions imposed by President Barack Obama. Zinke has ordered a review of a five-year offshore drilling plan to boost production.