Fox News' Judge Andrew Napolitano said the reason Trump "correctly" said D'Souza was treated "unfairly" is that "historically this has not been treated as a criminal prosecution".
Trump's pardon of D'Souza, who codirected the 2016 political documentary Hillary's America: The Secret History of the Democratic Party, comes out of the blue.
Trump also told reporters accompanying him to Texas that no one asked him to pardon D'Souza, whose case had become a cause in conservative circles.
Trump also pardoned Lewis "Scooter" Libby, former vice president Dick Cheney's chief-of-staff who was convicted of obstruction of justice and perjury, and Kristian Saucier, a US Navy sailor convicted of taking photos inside a nuclear submarine without permission.
Trump has pardoned other notable conservatives convicted of various offenses.More news: The startling viciousness of Pusha-T's Drake diss track
More news: 'Murdered' journalist Arkady Babchenko turns out to be alive
More news: ‘Kim Jong Un’ poses for selfies in Singapore
Though D'Souza fully admitted to knowingly violating the law, he lashed out at prosecutors at the time, arguing he was being singled out because of his conservative beliefs.
He has stirred controversy on social media for his offensive comments directed towards former President Barack Obama.
He was convicted of a felony, and spent eight months in federal custody.
Authorities said that he encouraged individuals to donate $20,000 to an unnamed political candidate - later revealed to be the New York Republican Wendy Long, who was challenging Democrat Kirsten Gillibrand for her Senate seat - which exceeded the federal campaign donation cap of $5,000. The judge said D'Souza had shown the court no evidence that he was targeted. Moreover, Mr. Obama's 2008 presidential campaign was itself fined $375,000 in 2013 for failing to disclose millions of dollars in contributions and missing deadlines for refunding millions in excess contributions.
A Justice Department spokesperson confirmed Thursday that Trump's pardon of D'Souza did not go through the department's Office of Pardon Attorney.
Preet Bharara, who brought charges against D'Souza when he was US Attorney for the Southern District of NY, asserted that there was no unfairness in the case.