He told his final news conference that "justice has been served".
Manning was sentenced to 35 years for leaking diplomatic cables to the group, one of the largest breaches of classified material in US history.
The commutation of her sentence has been attacked by Republicans as sending the wrong message.
House Speaker Paul Ryan said the move set a "dangerous precedent".
The 29-year-old transgender US Army private, born Bradley Manning, leaked documents to Wikileaks in 2010.
She will be freed on 17 May but had been scheduled to be released in 2045.