Scottish health secretary Shona Robison made the announcement at the conference of the Royal College of GPs, which is being held in Glasgow.
She said it would reduce the bureaucratic burden on GPs.
The news was welcomed by the British Medical Association, which is to be involved in developing a new contract for Scottish GPs.
Under QOF, thousands of pounds of GP income are tied to them delivering specific objectives.
Ms Robison said there will be transitional arrangements next year and a new contract in place for 2017.
She told the GPs: “I have always said I want to work with GPs in addressing the problems faced by the profession. Today I have announced that we will begin discussions to remove the outdated QOF system of payments for GPs, which I know many in the profession find bureaucratic and time-consuming.
“I have also given the conference a cast iron guarantee that we will not be following the UK Government’s plans to cut junior doctors’ pay. I know that the RCGP are particularly concerned the proposals and the growing confusion and alarm that this is causing trainees."
BMA Scottish GP committee chair Dr Alan McDevitt said the news was a "significant step."
He said: “It will have a positive effect on practices, by reducing workload and bureaucracy, allowing GPs to focus on the complex care needs of their patients.
“We believe that moving to a professionally driven, peer referenced system of quality will ensure that general practice and the NHS in Scotland continues to deliver a high standard of care to its patients.”
Researchers at Manchester University found a 10% reduction in satisfaction levels this year compared with 2012.
The national survey of GP working conditions has been conducted eight times since 1998 by the university's centre for health economics.
The survey found a slight reduction in the average GP working week - from 41.7 hours to 41.4 hours.
But GPs reported being stressed by increasing workloads and by growing pressure from "external bodies."
And a growing number of GPs stated their readiness to quit the profession.
Among doctors under the age of 50, this proportion rose from 8.9% to 13.1%.
Amongst those over the age of 50, some 60.9% expected to leave the profession within five years - compared with 54.1% three years ago.
The researchers say: "The 2015 respondents reported the lowest levels of job satisfaction amongst GPs since before the introduction of their new contract in 2004, the highest levels of stress since the start of the survey series and an increase since three years ago in the proportion of GPs intending to quit direct patient care within the next five years."
British Medical Association GP committee deputy chair Dr Richard Vautrey said the findings were "important."
He said: "It is no surprise that stress levels have reached their highest level for almost 20 years, as GP services are under unprecedented workload pressure against a background of mounting bureaucracy and falling resources.
“As the survey highlights, this has damaged GP morale and caused an increasing number of GPs to choose to leave the profession in the next five years – particularly worrying at a time when general practice faces a serious shortfall in the number of doctors choosing to train as GPs.
“Patients are understandably becoming frustrated at the lack of appointments and delays getting the treatment they need, but unless we turn this situation around the problem will get worse with too few GPs for the number of patients walking through our surgery doors."
The schools say they are seeking to head off a proposed boycott of the Foundation Programme by students graduating next year.
If the government continues with its proposed imposition of a new junior doctor contract, next year's graduates would be the first to work to the new arrangements.
But the Medical Schools Council says students who fail to take up Foundation Programme places will not be able to achieve full registration as doctors.
A near-identical letter has been circulated in 34 schools, provoking outrage among many students.
The letter says it is "essential" that students apply for a foundation post.
It says: "In particular, at this time, we advise you to adopt a professional attitude in your engagement with social media."
A spokesman for the Medical Schools Council said the letter originated in one medical school, which was concerned about a boycott of the Foundation Programme.
The spokesman said: "Subsequent emails, using some text from the initial note, were sent to medical students by medical schools. There have been critical reactions to some of these emails, particularly their reminder to be careful about the use of social media. This was a reference to GMC guidance on the subject.
"The Medical Schools Council emphasises that the original note was about the potential of a boycott of the Foundation Programme, and the negative impact that this could have on students’ careers.
"There was no suggestion that students should not comment on the contract proposals."
The new standard, published yesterday, will also reduce the extent of over-diagnosis of insignificant cancers by up to 89%, according to the European Association of Urology.
The guidelines were first released in draft form in December but the final version is updated and "simplified", according to its developers.
It sets out how the technique of multiparametric prostate Magnetic Resonance Imaging should be applied.
The guidelines have been developed by the American College of Radiology (ACR), the AdMeTech Foundation and the European Society of Urogenital Radiology.
Developer Professor Jelle Barentsz, of the Radboud University Medical Centre, Nijmegen, The Netherlands, said: “Early results have shown that mpMRI is an enormous help in detecting significant cancers.
"But to allow more wide-spread use, standardisation of image acquisition and interpretation is needed. The new PIRADS protocols have the potential to bring real benefits to many patients, throughout the world."
He added: "These MRI-scanners are big expensive beasts, but in fact we have also found that, when you consider the savings made by reducing unnecessary treatment, that mpMRI is cost-effective.
"We don’t suggest that mpMRI will completely replace the current ultrasound-biopsy method, but they are a powerful new diagnostic tool to the urologists in the diagnosis and treatment of prostate cancer."
Professor Hendrik Van Poppel, of the University of Leuven, Belgium, spokesman for the European Association of Urology, said: “PSA screening decreases prostate cancer mortality but exposes to overdiagnosis and overtreatment. mpMRI will not only simplify this screening, it will also play an important role in the follow-up of patients under active surveillance.
"It should be the first exam a patient at risk of significant prostate cancer should have."
PI-RADS Prostate Imaging – Reporting and Data System. European Urology in press; doi:10.1016/j.eururo.2015.08.052 [abstract]