Senate Republicans on Wednesday elected John Thune to be the next Republican leader to succeed Mitch McConnell in a position he's held for 17 years. In doing so, they decided against choosing Trump ally Sen. Rick Scott.

With McConnell announcing his intent to step aside earlier this year, Thune, the current Republican whip, was running against Sen. John Cornyn, a Texas senator and former Republican whip, and Scott, a Florida Republican who just won reelection to his second term.

In a statement, Thune said he was "extremely honored" and that the "Republican team was united behind President Trump's agenda."

"It's a new day in the United States Senate and it is a new day in America," Thune said at a press conference after the vote.

Thune introduced the new Senate GOP leadership team: Sen. John Barrasso as the majority whip, the No. 2 spot in leadership; Sen. Tom Cotton as Republican conference chair; Sen. Shelley Moore Capito as Republican policy committee chair; Sen. James Lankford as the Republican conference vice chair; and Sen. Tim Scott as the chair of the National Republican Senatorial Committee.

Thune was asked about whether he would move forward with Trump's demands for possible recess appointments of his Cabinet picks.

"Well, what we are going to do is make sure that we are processing his nominees in a way that gets them into those positions so they can implement his agenda. How that happens remains to be seen. Obviously, we want to make sure our committees have confirmation hearings like they typically do and these nominees reported out to the floor. But I've said this and I mean it, we expect a level of cooperation from the Democrat to work with us to get these folks installed."

"We're going to look at, explore all options to make sure that they get moved and they get moved quickly," Thune said.

Asked if the legislative filibuster would remain unchanged during his tenure, Thune replied "yes." The 60-vote threshold is a procedural rule requiring a supermajority to start or end debate on most legislation before a final vote.

Sen. Scott was eliminated after the first round of voting by secret ballot before the final round to elect Thune by a 29-24 vote.

Scott made appearances on cable news outlets in recent days and touted his endorsements from a number of Trump-aligned outside influencers, including Elon Musk and Robert F. Kennedy Jr. He tried to position himself as the most Trump-aligned candidate.

But Trump did not endorse Scott or any candidate in the leadership race, opting instead to insist that whoever was elected will support his use of recess appointments, which would allow him to temporarily fill federal vacancies without Senate approval.

All three candidates signaled their willingness to use that strategy to quickly fill out Trump's Cabinet.

ABC News Chief Washington Correspondent Jonathan Karl reported that sources said Trump did not endorse Scott because he didn't think he could win.

Ahead of the vote, Republicans gathered behind closed doors for over two hours Tuesday evening to hear arguments from Thune, Cornyn and Scott, as well as other senators who are running for down-ballot leadership positions. Any other candidate who might wish to throw their name in the running for party leadership would have been permitted to do so during the meeting.

It was described by senators in the room as "energetic," but not a debate.

When the meeting was over, Thune told reporters that Tuesday night was an opportunity for the conference to hear from the candidates.

When asked specifically about the whip count, Thune remained vague.

"You never know until the voters vote," Thune said.

Cornyn kept quiet leaving the room, "I'll make my pitch to my colleagues, not to you."

Even before the Tuesday meeting, the candidates were beginning to make their closing arguments and working to assert their loyalty to Trump, whose influence could certainly sway the outcome of the race.

Cornyn wrote a letter to colleagues Tuesday, obtained by ABC News, in which he repeatedly touted his commitment to Trump's agenda and confirmation of his Cabinet selections.

"It's imperative that Republicans hit the ground running to implement President Donald Trump's agenda for the American people," Cornyn wrote in the letter, citing GOP success across the House, Senate, an White House.

And Thune, who perhaps has had the iciest relationship with Trump among the contenders, also made clear he's been in regular contact with Trump's team, and he's made public statements supporting Trump proposals, including potential changes to Senate operating procedure.

Thune's Victory Signals Shift in Senate GOP

The election of Thune, who has served as the Senate's No. 2 Republican since 2019, marks a significant shift in the Senate's Republican conference. Many senators have been eager to move on from McConnell's long and powerful reign. Thune, however, will face a complicated test as he navigates a conference that is often divided over policy and tries to secure policy wins for Trump as he begins his second term.

Thune's Relationship with Trump

Thune has a history of disagreements with Trump, particularly after Trump's efforts to overturn the results of the 2020 presidential election and the Jan. 6, 2021 attack on the Capitol. Thune publicly criticized Trump's actions, calling them "inexcusable." However, in recent months, Thune has worked to smooth over his relationship with Trump, visiting him in Florida and consulting with him on how to implement his agenda.

What Lies Ahead for Thune?

Thune has pledged to work closely with Trump and has said that he will listen to Trump's demands. When Trump suggested that the new leader should allow him to appoint Cabinet members without Senate confirmation votes, Thune quickly responded that the Senate should "quickly and decisively" act to get nominees in place and that "all options are on the table to make that happen, including recess appointments."

Thune's victory is a testament to his experience, his ability to build relationships with colleagues, and his perceived ability to work with Trump. He will have a critical role in shaping the legislative landscape as Trump begins his second term.