The actions bring to 49 the number of people who Trump in the last two days has granted clemency either through pardons or sentence commutations.
The pardons of Manafort and Stone reward two of the most high-profile and widely condemned former advisers of the President, both of whom were indicted by special counsel Robert Mueller, went to trial and were convicted by juries of multiple crimes.
Reacting to Wednesday's pardons, Republican Senator Ben Sasse, in a six-word statement, said: "This is rotten to the core".
Paul Manafort, centre, arrives in court in NY in June 2019.
Among the people Mr.
The Manafort pardon spared the long-time Republican operative from serving the bulk of his 7-1/2-year prison term.
Roger Stone said he is praying for a full pardon from President Trump after others criminally charged in the US government's investigation of the 2016 elections were cleared of their convictions Tuesday.
Manafort worked on Trump's White House campaign for five months in 2016.
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John Boultbee and Peter Atkinson, who also received pardons, were part of the same fraud scheme as Conrad Black - the author of a glowing pro-Trump biography and the recipient of his own presidential pardon.
Prosecutors were never able to determine if Trump had learned in advance from Stone about planned releases from WikiLeaks of Democratic emails stolen by the Russians, and couldn't determine why Manafort shared internal campaign polls or discussed American policy in Ukraine with a Russian associate during Trump's run for office.
In a statement relayed by his lawyer, Manafort expressed his appreciation to Trump. One source told the news website that Trump said he would pardon "every person who ever talked to me". "Words can not fully convey how grateful we are", he said. Trump throughout his administration has shucked aside the conventions of the Obama administration, when pardons were largely reserved for drug offenders not known to the general public, and instead bestowed clemency on high-profile contacts and associates who were key figures in an investigation that directly concerned him.
Manafort was convicted as part of the special counsel probe into Russian meddling in the 2016 USA election.
Charles Kusnher was convicted in 2004 for tax evasion, illegal campaign contributions and witness tampering.
Kushner was prosecuted by Chris Christie when the former New Jersey governor was a US attorney for illegal campaign contributions, tax evasion and witness tampering.
Christie was quoted by CNN as saying Charles Kushner's case was "one of the most loathsome, disgusting crimes" he prosecuted.
A pardon in practice grants full legal forgiveness for a federal crime, as a result removing any remaining prison sentence, probation conditions or unpaid fines.