In a two-to-one vote judges with a provincial court ruled that Ola Bini should be freed while he defends himself against any upcoming charges.
The Swede thanked judges and the Ecuadorian people as he walked from from jail late Thursday night.
"Today we have proven my innocence for the first time and we will continue to prove my innocence," said Bini.
Bini was arrested at Quito's airport in April as he prepared to board a flight to Japan. Top Ecuadorian officials have alleged he was part of a plot hatched with two unidentified Russian hackers to threaten the release of incriminating documents regarding President Lenin Moreno.
Moreno was toughening his stance against Assange at the time, as frustration over his prolonged stay in Ecuador's London embassy under an asylum claim mounted. Bini is believed to have traveled at least 12 times to meet with Assange at the London embassy.
The 36-year-old expert on secure communications was detained hours after Assange's eviction. Authorities said he was carrying at least 30 electronic storage devices at the time. They ordered him detained for up to 90 days while they compiled evidence.
In brief comments to reporters at his hearing, Bini called the case against him in Ecuador "an illegal persecution."
"He hasn't committed any crime," Mario Melo, Bini's attorney, said. "He'll stay in the country until entirely demonstrating his innocence."
U.S. investigators have received permission from Ecuador to question Bini and are expected to speak with him on June 27th. It's not clear why American authorities asked to meet with him, however the request suggests that Bini may be seen as a potential witness or person of interest in U.S. investigations into Assange and WikiLeaks.
Privacy groups have accused Ecuador of carrying out a witch hunt because of Bini's friendship with Assange and his longstanding advocacy for digital privacy.
Bini arrived in Quito in 2013 after being transferred from Chicago to the Ecuador office of global tech firm Thoughtworks, which has guiding principles that stress social activism.