White House Chief of Staff Reince Priebus may have little left of his job but his title.
The former Republican National Committee chairman's dismissal marks the end to a tumultuous bid where he clashed with top advisors, most recently Scaramucci.
In his tweets, Trump called Kelly a great American, great leader and "a true star" of his administration.
Priebus had initially tried to block Scaramucci from an earlier post in the White House.
Mr Scaramucci's verbal tirade was made during a phone conversation with The New Yorker's Washington correspondent Ryan Lizza on Wednesday night.
In that report, Scaramucci seemed to accuse Priebus of leaking information to the media and called him a "paranoid schizophrenic, a paranoiac".
Following his eventual appointment last week, press secretary Sean Spicer - a Priebus ally - resigned in protest.
It also comes a week after Trump hired Wall Street businessman Anthony Scaramucci, a move that sparked a long-rumored shake-up among the president's top aides. That left Priebus with the blame for numerous administration's legislative stumbles, including during the arduous attempts at passing a bill to repeal and replace Obamacare - which Priebus had advised Trump to make his first legislative priority, promising him swift victory. Scaramucci tagged Priebus in the tweet, but he later denied that he was identifying Priebus as the source. But the tornado of Trump only got stronger, and no amount of plywood and nails would keep the house in order. He channelled Priebus as he spoke: " 'Oh, Bill Shine is coming in.
That didn't mean he wasn't critical. The issue, he said, was that he believed Priebus had been anxious about the dinner because he hadn't been invited.
But Priebus had to temper his criticisms throughout the campaign, so he didn't suffer Trump's wrath - and the party didn't implode.
He told CNN on Thursday that "if Reince wants to explain he's not a leaker, do that".
Priebus wound up winning over Trump.
A tax overhaul hasn't materialized, despite pledges of addressing it by the summer.