The humpback whale stunned scientists when it was spotted in the crocodile infested waters of Kakadu.
"After monitoring the whale this weekend, we're delighted to see it has made its way out of Kakadu's East Alligator River and into Van Diemen Gulf," Feach Moyle, Manager Country and Culture Section at Kakadu National Park told NITV in a statement.
"The whale made its way out on the high tides of this weekend, and we're pleased it appeared to be in good condition and not suffering any ill effects."
Three whales were first spotted in the East Alligator River by marine biologist Jason Fowler on September 2. By late last week, two of the trio had made their way back out to sea.
It is believed that humpback whales have never entered the river before, and since whales get around using sight and sound, the murky waters caused some confusion.
Traditional Owners, Parks Australia staff and scientists from around the country worked together to monitor and assist the lost whale.
NT government scientist Dr Carol Palmer was a member of the emergency response team and told NITV News the whale's exit is "great news".
"It's been fantastic working with staff at Kakadu as well as expert scientists to identify ways to assist the whale, but I'm very happy it has found its own way," said Dr Palmer. "This is the very best outcome we could have hoped for."
Earlier last week, Dr Palmer told the ABC the team was considering using whale calls to help guide the whale back out to sea, creating underwater noise pollution could discourage them from heading further up the river. Orca (killer whale) sounds have proven successful in similar situations.
To avoid adding further danger to the whales, a boat exclusion zone of 30 kilometres from the river mouth was set up by the NT government and federal authorities.
Experts are still unsure why the whales chose to take the muddy detour on the way to their annual feed in Antarctica.