Stone had been set to serve 40 months in prison for the crimes of lying to Congress, obstruction and witness tampering.
His conviction was linked to a justice department probe into allegations that Russia interfered in the 2016 presidential elections.
But Mr Trump said that Stone, the sixth of his associates to be found guilty on charges linked to the investigation, had been the victim of a "hoax."
The White House said in a statement: "Roger Stone is a victim of the Russia Hoax that the Left and its allies in the media perpetuated for years in an attempt to undermine the Trump Presidency."
The statement said that the Russia investigation switched to focus on "high-profile people" in the president's circle out of frustration that it couldn't prove the "fantasy" that Mr Trump's campaign colluded with Russia.
The White House went on: "These charges were the product of recklessness borne of frustration and malice. This is why the out-of-control Mueller prosecutors, desperate for splashy headlines to compensate for a failed investigation, set their sights on Mr. Stone."
Mr Trump also suggested that the FBI had told CNN about the raid on Stone's house ahead of time, noting that a camera crew was present.
The statement added: "Roger Stone has already suffered greatly. He was treated very unfairly, as were many others in this case. Roger Stone is now a free man!"
Stone has long appealed for help from the president, begging for clemency in a series of social media posts. He has always denied any wrongdoing and said his conviction was politically motivated.
Mr Trump has commented publicly on Stone’s case several times, including just before sentencing, when he suggested that Stone was being held to a different standard than several prominent Democrats.
He said in a tweet that the conviction “should be thrown out” and called the Justice Department’s first sentencing recommendation “horrible and very unfair”.
“Cannot allow this miscarriage of justice!” he added.
Mr Trump's intervention came after a court of appeal said Stone, 67, could not delay the start of his sentence.
The move to commute Stone's sentence, which stops short of a full pardon, has outraged Mr Trump's political opponents.
House of Representatives Intelligence committee chairman Adam Schiff, a Democrat, hit out at the president's intervention.
He said: "With this commutation, Trump makes clear that there are two systems of justice in America: one for his criminal friends, and one for everyone else."
And Democratic National Committee Chair Tom Perez said: "Is there any power Trump won't abuse?"