Senators voted 52-46 to approve Oklahoma Attorney General Scott Pruitt, who Senator John Barrasso, a Republican and the head of the chamber's environment committee, said would reform and modernize the EPA.
Republicans have said the agency has killed jobs in coal and in oil drilling by limiting emissions and nearly all Republican senators voted for him.
Pruitt is expected to be sworn in quickly and next Trump likely will issue executive orders to reshape the EPA, sources said.
Pruitt's nomination was controversial in progressive circles. He sued the agency he intends to lead more than a dozen times while top prosecutor of his oil and gas producing state, and has expressed doubts about the science behind climate change.
Democratic Senator Ben Cardin said he was concerned Pruitt's opposition to Obama's landmark Clean Power Plan to reduce emissions from coal and natural gas burning plants would hurt the environment and U.S. leadership in international efforts to curb climate change.
Other opponents of Pruitt's nomination expressed concerns about his ties to the energy industry. Democrats tried to extend debate on Pruitt until late February when emails between him and energy companies will likely be revealed by a judge, but the effort failed.
An Oklahoma court ruled this week that Pruitt will have to turn over 3,000 emails between his office and energy companies by Tuesday after a watchdog group, the Center for Media and Democracy, sued for their release.
Senate Minority Leader Chuck Schumer told reporters that Majority Leader Senator Mitch McConnell had moved to "strap blinders" on his fellow Republicans by not waiting for the release of Pruitt's emails.
Two Democrats from energy-producing states, Joe Manchin of West Virginia and Heidi Heitkamp of North Dakota, voted for Pruitt.
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