Mr Manafort was convicted in 2018 in an investigation into alleged Russian meddling in the 2016 US election.
Mr Trump had previously commuted the prison sentence of Mr Stone, who was convicted of lying to congress.
They are among 29 people to benefit from Mr Trump’s latest pardons before he leaves office next month.
Twenty-six of them won full pardons on Wednesday night, 23 December, 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.
A pardon is an expression of the president’s forgiveness that confers extra privileges such as restoring the convict’s right to vote.
Presidents often grant pardons in their final days of office.
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 himself.
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 and I humbly thank you for the Presidential Pardon you bestowed on me, words cannot fully convey how grateful we are.
Stone was found guilty of lying to congress about his attempts to contact Wikileaks, the website that released damaging emails about Mr Trump’s 2016 democratic election rival Hillary Clinton.
On Wednesday night, the long-time Trump friend and adviser welcomed his upgrade from a commutation to a full pardon.
Stone has been urging Mr Trump on his way out of the white house to also pardon Wikileaks co-founder Julian Assange and national security agency leaker Edward Snowden.
Another pardon went to Charles Kushner, a real estate magnate who is the father of Ivanka Trump’s husband, Jared Kushner.
Kushner 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 retaliation against his brother-in-law who was cooperating with authorities against him. Kushner hired a prostitute to seduce his brother-in-law, recorded their encounter with hidden cameras and sent it to his own sister.
It is the president’s second wave of clemency orders in as many days, on Tuesday night he pardoned 15 people and bestowed commutations on five others.
The constitution gives the sitting president the power to grant reprieves and pardons for offences against the United States, except in cases of impeachment.
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