The move allowed Oklahoma Attorney General Scott Pruitt's nomination to proceed despite Democrats' second consecutive day skipping out on the scheduled vote.
Republicans unanimously approved Pruitt, 11-0.
"It's disappointing that they chose that course of action but we will not allow it to obstruct," the Environmental Public Works Committee Chairman Sen. John Barrasso said.
Republicans on the Senate Finance Committee employed the same maneuver Wednesday after Democrats also boycotted votes on the nominations to head the departments of treasury and health and human services.
Barrasso slammed Democrats' move as "unprecedented."
"Elections have consequences and the new President is entitled to put in place members to his agenda. Now it is time to set up a functioning government. That includes a functioning EPA," Barrasso said before moving forward with the committee vote.
Republicans also voted to approve a funding resolution with Democrats absent from the committee.
Democrats on Wednesday said they chose to boycott the vote because the EPA nominee had yet to answer some of the questions they had submitted to him in writing.
"If Scott Pruitt is serious about serving as our next EPA administrator, he should be more than willing to provide @EPWDems complete answers," Democratic Sen. Tom Carper of Delaware tweeted Wednesday shortly after the first boycott.
"We have a right and a responsibility to examine and critically evaluate these nominees' background, to make sure that they will fulfill their oath and their responsibility," Sen. Kamala Harris, a California Democrat, said at a news conference outside the hearing room on Wednesday. "This is about transparency in government. This is about dealing with the fact that you think the system is rigged."
Republicans, meanwhile, knocked Democrats for submitting 1,078 questions and Barrasso on Thursday insisted the committee had thoroughly vetted Pruitt.