This is Trump's fifth pardon. He also investigated unfounded claims, supported by Mr Trump, questioning Mr Obama's citizenship.
President Donald Trump was signaling to former embattled associates, and even special counsel Robert Mueller, the "awesome powers" he holds in office with his pardon of a conservative commentator and suggestion of two other pardons, according to longtime adviser Roger Stone.
In 2014 D'Souza pleaded guilty to making illegal campaign contributions to the failed Senatorial campaign of New York Republican Wendy Long; he was sentenced to eight months in a halfway house and five years of probation for the felony, and ever since has gone on about how unfairly he was treated for a crime he admitted to committing. Trump said she was "unfairly treated" and "used to be my biggest fan in the world".
In 2014, when he was charged with violating federal election campaign laws, D'Souza alleged that he was the victim of selective prosecution, targeted for his conservative beliefs.
Trump tweeted Thursday: "Will be giving a Full Pardon to Dinesh D'Souza today". Stewart went to jail after former FBI director and federal prosecutor James Comey led the investigation into her suspect stock sale in 2004.
Blagojevich was convicted for corruption for a number of actions, including an attempt to sell the U.S. Senate seat that was vacated by now-former President Barack Obama. In 2012 his movie "2016: Obama's America's" which was based on his anti-Obama book became the second-highest-grossing political documentary film produced in the U.S.
D'Souza said Friday on "Fox & Friends" that Trump called him on the phone and told him, "I gotta tell you man to man: you got screwed" and that a "great injustice had been done".
Trump also said he might commute the 14-year prison sentence of former Illinois Governor Rod Blagojevich, a Democrat convicted of corruption charges, and was considering pardoning a woman convicted of a drug-related charge after reality TV star Kim Kardashian discussed the case with him on Wednesday.
Regarding Blagojevich, Trump said he was considering commuting his sentence, which he described as "really unfair" punishment for "foolish" behavior.
Both cases prompted critics to accuse Mr Trump of abusing his pardoning power.
On Thursday, D'Souza thanked Trump in Twitter posts that also slammed Bharara.
White House spokesman Raj Shah echoed D'Souza's claim of selective prosecution. The origin of the pardon dates back hundreds of years to English monarchy, said Steven Schwinn, an expert in constitutional law and a professor at the John Marshall Law School.
Previously Trump has pardoned former Arizona sheriff Joe Arpaio, a Trump supporter convicted of criminal contempt of court, the late boxer Jack Johnson and a former sailor, Kristian Mark Saucier, who was convicted of unauthorized use of classified information.
Susan Hennessey, a fellow in national security in governance studies at the Brookings Institution, acknowledged on CNN that the president has unreviewable pardon authority.