Neill, 34, had joined the Abu Dhabi club on an initial one-year deal last summer, but after an inconsistent season Jazira have opted against extending the Australian international's stay.
The news was confirmed by Hamad Al Suwaidi, a member of the Jazira's board of directors, who aslo revealed that coach Caio Junior would be joining Neill out of the exit door at the Mohammed bin Zayed Stadium.
The Brazilian, who succeeded Franky Vercauteren in March, led the club to President's Cup success with a 3-1 win over Bani Yas and the last 16 of the AFC Champions League for the first time in their history.
However, defeat to Saudi Arabia's Al Ahli in their Asian clash and disappointing results in the Pro League as Jazira, 2011 champions, finished fourth, has been Junior's downfall.
Neill's exit, meanwhile, comes as no real surprise with the veteran Socceroo skipper struggling for form and consistency since arriving in the UAE capital.
However, the player himself had hinted to Sport360° last month that he was keen on staying at the club. "I’ve been really pleased with the way things have gone and really excited for the future too," he said.
“My contract comes to an end soon. There are a lot of things happening. I’ve got World Cup qualifiers to look forward to. So, all in all, I think this season has been a wonderful one both on and off the pitch.”
He is now lo the lookout for a new club, though, with rumours already abound that Saudi club Al Nassr are keen on his signature, while a return to England where he spent 15 years with Millwall, Blackburn, West Ham and Everton, could also be an option.
The highlight of his time in the UAE will scoring the opening goal in Jazira's President's Cup final back in April with Neill calling it the "most important goal of his career".
However, he will perhaps best be remembered for his decisive miss in his side's penalty shootout defeat to Ahli last month which saw them crash out of the Champions League.
Meanwhile, as Neill leaves, his defensive partner Juma Abdulla has signed a three-year contract extension with the club who have also brought in Hamad Al Hammadi, a 23-year-old defender from Al Dhafra, on a three-year deal.