D'Souza was prosecuted by Preet Bharara, a former U.S. Attorney in NY who became a bitter Trump opponent after the president fired him, along with dozens of other federal prosecutors, upon taking office.
Critics believe the US president's motivation for pardoning these particular public figures is to send a message to the US Department of Justice and the FBI amid as Robert Mueller continues special counsel investigation.
D'Souza had claimed selective prosecution before pleading guilty.
This would be Mr Trump's fifth full pardon.
Speaking to reporters on Air Force One, Trump complained that Stewart had been "harshly and unfairly treated".
President Trump said Thursday that he is considering commuting the sentence of former Illinois Gov. Rod Blagojevich and pardoning style maven Martha Stewart, potentially taking his unorthodox use of pardons to new heights. He also noted that Blagojevich is a Democrat.
Trump said the disgraced politician was behind bars 'for being stupid and saying things that every other politician - you know that many other politicans say'.
Mr. D'Souza also slammed Mr. Bharara in a series of tweets after he was pardoned and alleged that one Indian American had tried to destroy the career of another Indian American. He is also a former commentator on NPR.More news: Kerala CM Pinarayi Vijayan announces Re 1 cut in fuel prices
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"I knew that causing a campaign contribution to be made in the name of another was wrong and something the law forbids", D'Souza said at the May 2014 hearing.
His star in this vein rose to new heights during the Obama administration, which he cast in his political work as a diabolical anti-colonialist engine created to cripple the United States.
D'Souza thanked those who urged Trump to pardon him, and took a swipe at Preet Bharara, the US attorney who prosecuted him.
Prosecutors said D'Souza had other individuals donate money to Republican Wendy Long, a Republican who was challenging Sen. "I can not believe how stupid I was, how careless, and how irresponsible", D'Souza wrote in a statement to the judge.
D'Souza was sentenced to five years of probation, including eight months' confinement in a community center. Trump fired Bharara from the US attorney job after initially promising Bharara that he would stay on in the new administration.
He said that he spoke to D'Souza for three minutes on Wednesday night to tell him about the pardon and "he nearly had a heart attack".
"It's nearly like President Trump went through a list of potential crimes that he and his White House could be charged with and found pardons for other people to lay the groundwork", he said on CNN. Here's a look at the pardons President Donald Trump has granted during his presidency: August 25, 2017: Trump pardoned former Maricopa County Sheriff Joe Arpaio's criminal contempt-of-court conviction for intentionally disobeying a judge's order in an immigration case. Barack Obama became president.
While issuing pardons used to be more common, presidents in the past few decades have waited until closer to the end of their terms before granting large amounts of pardons, particularly those that might be considered controversial.