Stone was due to report to a federal prison in Jesup, Georgia, next week to begin a 40-month prison term.
He has been convicted by Department of Justice prosecutors under special counsel Robert Mueller of lying to Congress, obstruction and witness tampering.
“Roger Stone was targeted by an illegal Witch Hunt that never should have taken place. It is the other side that are criminals, including [Joe] Biden and [Barack] Obama, who spied on my campaign - AND GOT CAUGHT!,” Trump tweeted Saturday morning.
Stone is the latest offender from a long list figures tied to Trump, whose prison terms have been been pardoned by him.
Other offenders who were pardoned by Trump include former Illinois Gov. Rod Blagojevic, former New York City Police Commissioner Bernard Kerik and financier Michael Milken.
Lawmakers on both sides of the aisle slammed Trump for favoritism, accusing the president of setting up an alternate system of justice for his allies.
“The American ideal of equal justice under the law is once again being undermined by a lawless president who regards the Justice Department as his personal plaything,” said Senate Minority Leader Charles Schumer (D-NY).
"Unprecedented, historic corruption: an American president commutes the sentence of a person convicted by a jury of lying to shield that very president," Senator Mitt Romney (R-UT) tweeted.
Trump commuted the prison sentence of Stone on Friday, sparing his longtime ally from going to jail.