"The president said 'Dinesh, you've been a great voice for freedom". He also investigated unfounded claims, supported by Mr Trump, questioning Mr Obama's citizenship.
The right-wing provocateur was sentenced to five years' probation, including eight months in a halfway house, after pleading guilty in 2014 to illegally using straw donors to contribute to Republican Wendy Long, who challenged US Sen. "He was treated very unfairly by our government!"
D'Souza had plead guilty in 2014 to federal campaign finance law violations.
James Comey, whom Trump fired as FBI director a year ago and has repeatedly assailed, was the lead federal prosecutor in Stewart's case and played a role in the prosecution of Lewis "Scooter" Libby, the chief of staff to former Vice President Dick Cheney.
Trump announced one pardon Thursday and said he was considering two others.
Blagojevich and Stewart also appeared on versions of Trump's former reality show "The Apprentice".
"Donald Trump has sent a message to his friends and cronies that if you break laws to protect him or attack our democracy, he's got your back", said David Donnelly, president and CEO of Every Voice.
The president added that it was "stupid" for Blagojevich to have said what he did regarding selling off former President Barack Obama's vacated U.S. Senate seat in 2008, but that the sentence Blagojevich is now serving was too harsh.
Mr Trump told reporters on Thursday aboard Air Force One that Stewart, best known as a famous homemaker and TV personality, was "to a certain extent ... harshly and unfairly treated". His 2010 book "The Roots of Obama's Rage" was made into a film, "2016: Obama's America", which was popular with conservative groups.
"Trump's action sends yet another risky signal that he will abuse his power to protect those who would subvert the rule of law, including the laws that protect the integrity of our democracy from corruption", Flynn said.
He said he is weighing a pardon for Martha Stewart, who served time for conspiracy and lying to federal investigators but has been free for more than a decade.
The president also said he is also considering commuting the sentence of former Illinois Governor Rod Blegojevich.
After D'Souza's pardon, some constitutional scholars, legal analysts and Democratic lawmakers accused Trump of undermining the rule of law with pardons based on political considerations. If you've followed D'Souza's career you know that he's just the dullest kind of partisan hack-one without even the bad sense of humor or weirdly enraging anti-charisma of a Sean Hannity or Ann Coulter.
Trump last week posthumously pardoned boxer Jack Johnson, the first black world heavyweight champion, who was jailed a century ago because of his relationship with a white woman.
Also pardoned was former White House aide I. Lewis "Scooter" Libby.
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.