Stone, one of Trump's oldest confidants, was convicted last November of lying to Congress, tampering with a witness and obstructing the House investigation into whether the Trump campaign conspired with Russia to help him win the 2016 election.
The fiery White House statement reiterated Trump's charge that Special Counsel Robert Mueller investigated an alleged crime that was never committed. It argued that Stone should therefore never have been charged in the first place.
"The simple fact is that if the Special Counsel had not been pursuing an absolutely baseless investigation, Mr Stone would not be facing time in prison," it said.
In a statement to US media, Stone's lawyer Grant Smith said his client was "incredibly honored that President Trump used his awesome and unique power under the Constitution of the United States for this act of mercy."
The Trump administration had already intervened once to help Stone. After prosecutors recommended a prison term of seven to nine years, Attorney General Bill Barr, who has been accused of acting like Trump's personal lawyer, stepped in and called that excessive.
All four prosecutors handling the case quit it and a newly appointed prosecutor recommended a prison term of three to four years for Stone.
Stone was the sixth aide of Trump - who was impeached last year for abusing his power - to be convicted of charges arising from Mueller's probe into Russian election interference.
Former Trump campaign manager Paul Manafort released from prison early due to coronavirus risk
State Department inspector general Steve Linick was removed last month after running a misconduct probe into Washington's top diplomat and steadfast Trump ally Mike Pompeo.
More than 1 000 former Justice Department officials signed a statement calling for Barr's resignation over his interference to get a lighter sentence for Stone.