Manafort was convicted in 2018 in an investigation into alleged Russian meddling in the 2016 US election.
Trump has previously commuted the prison sentence of Stone, who was convicted of lying to Congress.
They are among 29 people to benefit from Mr Trump’s latest clemency spree before he leaves office next month.
Twenty-six of them received full pardons while another three received commutations.
A commutation usually takes the form of a reduced prison term, but does not erase the conviction or imply innocence.
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A pardon is an expression of the president’s forgiveness that confers extra privileges such as restoring the convict’s right to vote or serve on juries.
Presidents often grand pardons in the final days of office, and Mr Trump has used the power more sparingly than any president in modern history apart from George HW Bush.
Mr Trump’s pardon for Manafort spared his former campaign chairman from serving most of his seven-and-a-half year prison term for financial fraud and conspiring to obstruct the investigation into him.
He had been serving his term under home confinement since being released from federal prison in May over fears of coronavirus, but is now a free man.
The grateful political operative responded by tweeting: “Mr President, my family & I humbly thank you for the Presidential Pardon you bestowed on me. Words cannot fully convey how grateful we are.”
Another pardon went to Charles Kushner, a real estate magnate who is the father of Ivanka Trump’s husband, Jared Kushner, a White House adviser.
Kushner Snr whose family boasts a portfolio of 20,000 properties from New York to Virginia was sentenced to two years in prison in 2004 for charges including tax evasion, campaign finance offences and witness tampering.
The witness tampering charge arose from Kushner Snr’s retaliation against his brother-in-law, who was co-operating with authorities against him. Kushner Snr hired a prostitute to seduce his brother-in-law, recorded their encounter and sent it to his own sister.
Former Trump adviser Chris Christie, who as a New Jersey prosecutor jailed Kushner Snr, told CNN it was “one of the most loathsome, disgusting crimes” he had come across.
It was the president’s second wave of clemency orders in as many days. On Tuesday night he pardoned 15 people and gave commutations to five others.
They included two other figures who were convicted in the US special counsel inquiry into alleged Russian election interference, three ex-Republican members of Congress, and four Blackwater military contractors who were involved in a 2007 massacre in Iraq.
In November, Mr Trump pardoned former National Security Adviser Michael Flynn, who was also convicted in the special counsel’s Russia inquiry.
Mr Flynn had admitted lying to the FBI before attempting to retract his guilty plea.
Special counsel Robert Mueller’s 22-month inquiry concluded in May last year that it could not determine Mr Trump or any of his aides had colluded with the Kremlin to sway the 2016 election in his favour. Mr Mueller did not accuse any Trump associate of conspiring with Russia.
The president regularly condemned the investigation as a witch hunt and he has now pardoned five figures convicted as a result of that probe.
Notably left out of Mr Trump’s wave of Christmas pardons are two other figures who were convicted in the Mueller probe: Manafort’s deputy, Rick Gates, and former Trump lawyer Michael Cohen.
Both men co-operated extensively with prosecutors.
Cohen, who was released from prison in May over coronavirus concerns, took to Twitter to vent about the pardons.
“What happened tonight shows how broken the whole criminal justice system is,” he tweeted.
Source: BBC
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