Delays in answering calls have resulted in the helpline resorting to using its previous system after just 10 days.
Once a solution to the problems is found, the programme will be re-launched - expected to be early 2016.
The call-handling and IT system - called the Future Programme - "has proved extremely challenging", according to an NHS statement.
This is despite "a huge amount of planning, system testing and staff training".
NHS 24 chief executive Ian Crichton warned that keeping the Future Programme in service at this level of operation would be unsafe for patients.
He said he expected the volume of calls the helpline receives over the weekend to "significantly increase" as winter approaches, which indicates that the service "would fall below acceptable tolerances".
"This is not a decision that we have taken lightly, given the significant investment to date, but one that will ensure we can continue to deliver vital and safe out-of-hours support to patients when they need it most during the coming winter",  he said.
The NHS will continue to develop the new system offline before rolling it out again early in the new year.
Scottish Labour's public services spokeswoman Jackie Baillie accused the Scottish government of having a "short-term, sticking plaster approach to the NHS".
Scottish Conservative health spokesman Jackson Carlaw called the project "a mismanaged shambles" which had cost the taxpayer a fortune.
Health Secretary Shona Robison said that while NHS 24 remained fully operational, she was disappointed that it had to revert to the previous system.
However, she said patient safety was the priority and "it is right that NHS 24 take the time necessary to understand and fix any outstanding problems completely".
Theresa Fyffe, Royal College of Nursing Scotland director, said it was "regrettable" but "the right decision" for patients and staff.
The announcement follows an incident in October, when the same system crashed and staff had to resort to pen and paper.
An Audit Scotland report had also previously raised concerns over the cost and delivery of the system.
Initially due to be ready for October 2013, it was delayed for two years and cost about £117m - almost £40m above the expected cost.

Taylor beat Van Gerwen in the opening contest, but Lewis then struggled in losing to Van Barneveld, before the Dutch won the pairs.
But Taylor's defeat of Van Barneveld forced a decider, in which Lewis beat Van Gerwen 4-1.
Victory in Frankfurt gave England their fourth World Cup of Darts crown.
After losing both of his matches in the final, world number one Van Gerwen seemed to take exception to Lewis' celebrations on sealing the trophy.
"MVG got the the hump with me because I gave it large, but I said to him that he does that every week, so he has to expect some back," said Lewis.
Taylor and Lewis, both from Stoke-on-Trent, had earlier defeated Northern Ireland duo Brendan Dolan and Daryl Gurney in the semi-finals.
Scotland, represented by world champion Gary Anderson and Robert Thornton, lost in the quarter-finals to Belgium.
The medical helpline NHS 24 has shelved a new £117m phone system over fears for patient safety.
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England pair Phil Taylor and Adrian Lewis retained the World Cup, beating the Netherlands' Michael van Gerwen and Raymond van Barneveld in the final.