Police say the case will remain open, but all staff working in the investigation have been deployed to other duties.
Detective Inspector Mark Benefield, the officer in charge of the investigation, said the case will no longer be active unless new information is received.
"We have explored hundreds of theories and a number of leads and I am confident that, if we get the right information from the right people in due course, we will be able to tell Jane's family who was responsible for her disappearance and death."
Mr Benefield thanked everyone involved in the investigation over the last two years, and paid tribute to the media for keeping Furlong's story alive.
Police have informed Furlong's mother, Judith Furlong, of the impending wind-down last month.
The information hotline, 0800 675 263, will remain operational for a few more weeks.