Republicans have elected Senator Thune as the next Senate majority leader, completing a momentous shift in their leadership that elevates a top deputy of Senator McConnell into a key position as President-elect Trump returns to the White House.

Mr. Thune, 63, is in his fourth Senate term representing the state of South Dakota and has promised to work closely with Trump, despite differences the two have had over the years, and will be a crucial part of the incoming president’s efforts to push through his policy agenda.

He beat out two other competitors, Senators Cornyn and Scott, by gaining majority support from GOP senators in a secret ballot vote. Republicans are replacing Mr. McConnell, the longest serving Senate party leader, as they prepare to take majority control of the Senate with the 53 seats they won in last week’s elections.

Like Mr. McConnell, Mr. Thune hails from the Republican Party’s more traditional wing. He has held the Republican whip position — no. 2 in party leadership — since 2019.

At times, Mr. Thune has countered Trump’s wishes for Congress, and he broke publicly with Trump over the effort to overturn the results of the 2020 presidential election, which he called “inexcusable.” But in recent months, Mr. Thune has realigned with Trump, visiting him in his Florida home, and the two have been consulting on how to implement the incoming president’s agenda.

Mr. Thune told The Associated Press over the summer that he views their potential relationship as a professional one. If they both win their elections, he said, “we’ve got a job to do.”

Well liked and a respected communicator, Mr. Thune has been perceived as a front-runner for much of the year. As the No. 2 Republican, he took over for Mr. McConnell for several weeks last year when he was on a medical leave. He is also a former chair of the Senate Commerce Committee.

Mr. Thune’s win is all the more extraordinary because of his 2004 election to the Senate — defeating then-Senate Majority Leader Tom Daschle after arguing during the campaign that Mr. Daschle had lost his South Dakota roots during his years in Democratic leadership. Twenty years later, Mr. Thune will become majority leader himself.

As he geared up to run for leader, Mr. Thune spent much of the year campaigning for his colleagues. According to his aides, he raised more than $31 million to elect Senate Republicans this cycle, including a $4 million transfer from his own campaign accounts to the Senate’s main campaign arm.

This year, though, Mr. Thune and Trump have talked frequently on the phone and Mr. Thune visited the then-GOP candidate at his home in Florida.