The questioning took place in the Ecuadorian Embassy in London, where the 45-year-old Australian has been holed up since 2012 to avoid extradition to Sweden.
"After UN & court findings condemning 6 years of abuses by Sweden against Assange, Sweden finally takes his statement for the first time ever," the official WikiLeaks account tweeted.
Wikileaks also released a statement Monday, complaining that Assange's Swedish lawyer, Per Samuelson, was not notified or summoned to attend the session, which it called a "clear breach of process."
The statement said that there were many "irregularities in Sweden's preliminary investigation, which the UN has described as 'excessive and unnecessary' ."
"Sweden's failure to progress the preliminary investigation until now has resulted in a gross breach of Mr Assange's right to be presumed innocent and has fatally harmed his ability to meaningfully defend himself," the statement said.
A throng of journalists awaited Swedish prosecutor Ingrid Isgren as she arrived at the embassy Monday to attend the questioning of Assange on the sexual assault allegations made by two female WikiLeaks volunteers in Sweden.
Under the arrangement made between Sweden and Ecuador -- the result of years of complicated diplomatic and legal negotiations -- Sweden prepared a list of questions for an Ecuadorian prosecutor to ask Assange and his legal team in the presence of Isgren and a Swedish police investigator.
A DNA sample was also to be taken during the visit, subject to Assange's consent, according to the terms of the arrangement.
After the questioning, Ecuadorian officials would file a report on the interview to the Swedes, who would then decide whether or not to file charges.
Isgren left the embassy more than three hours after she arrived Monday, and returned about an hour later.
Long legal saga
The interview is the latest twist in a long legal saga that has played out since Swedish prosecutors first issued an arrest warrant for Assange in August 2010, and began seeking his extradition.
Assange, who has denied the sex assault allegations, has said he fears extradition
to Sweden could result in another extradition to the United States, where he could face the death penalty if he is charged and convicted of publishing government secrets through WikiLeaks.
After British courts ruled in support of Assange's extradition to Sweden, Ecuador granted the WikiLeaks founder political asylum in August 2012.
This year, Assange's legal team has intensified its calls for Sweden to adhere to a non-binding opinion by the United Nations working group on arbitrary detention, which stated in February that his confinement in the embassy should be considered as arbitrary detention enforced by Sweden and Britain.
But in September, a Swedish court ruled that the arrest warrant for Assange on allegations of rape still stood -- the eighth time the European arrest warrant had been tested in a Swedish court.
A small group of Assange supporters gathered outside the embassy Monday.
Once a hero to many on the left, Assange has faced criticism for WikiLeaks' intervention in the US presidential election, releasing a trove of hacked emails from Democratic organizations and figures that were damaging to Hillary Clinton's campaign.
The Obama administration said it was confident Russia was behind the hacks, and Ecuador temporarily cut off Assange's Internet access
in the embassy in response to his activities.
Many of Assange's supporters have called on President-elect Donald Trump to pardon Assange when he takes office. But despite Trump having claimed "I love WikiLeaks" on the campaign trail, it is unclear whether Assange's fortunes will change under his presidency.