The outgoing US president used his final hours in the White House to commute the sentence of the former soldier jailed for 35 years for handing over classified documents to Wikileaks.
The former intelligence analyst said she had passed on government and military documents to raise awareness about the impact of war.
Assange, who has been living at the Ecuadorian embassy in London since the summer of 2012 due to fears he will be extradited to the US, praised campaigners for their role in the Manning decision, the Press Association reported.
He said: “Thank you to everyone who campaigned for Chelsea Manning’s clemency. Your courage & determination made the impossible possible.”
Melinda Taylor, a member of Assange’s legal team, insisted previous comments made about the implications of the Manning case still stand.
“Everything that he has said he’s standing by,” she said.
Manning’s planned release in May, following seven years of incarceration, appears to pave the way for the Wikileaks founder’s self-imposed exile to come to an end.
The organisation last week tweeted:
Assange was interviewed in the embassy in November in the presence of prosecutors from Sweden, where he faces a sex allegation.
He denies the claims, but believes he will face extradition to the United States - for questioning over the activities of WikiLeaks - if he leaves the embassy.
But while many praised Obama’s decision to free Manning, there seemed to be little sympathy for Assange...
Manning attended Tasker Milward comprehensive in Pembrokeshire and still has family and friends in the area.
Conservative former Cabinet minister Stephen Crabb praised Obama for showing “mercy” in a complicated case.
The Preseli Pembrokeshire MP said: “I think the actions of President Obama reflect extremely well on him. He has shown compassion and mercy. This was clearly not a straightforward case.”
WikiLeaks later tweeted: “Assange is confident of winning any fair trial in the US. Obama’s DoJ prevented public interest defense & fair jury.”