Following negotiations between the GPC and NHS Employers, GMS practices will receive a 0.5% overall funding uplift to cover rising staff costs.
GPC chairman Dr Laurence Buckman said he was 'pleased the government has recognised the need to increase practice expenses', but said the long delay in announcing the deal was 'unacceptable'.
The DoH said the uplift should be used to fund £250 pay rises for practice staff earning less than £21,000 a year, but GP pay should not change.
The increase will be delivered by increasing the value of QOF points from £127.29 to £130.51. Accountants said the uplift was worth around £3,000 to an average practice.
As part of the deal, the extended hours DES scheme will continue, but funding for it will fall by £60 million.
Practices will be expected to open for the same number of hours, but receive £1.90 instead of £3 per registered patient.
GPs will be able to complete extended hours opening requirements in half-hour blocks, with the minimum 1.5-hour extended opening rule dropped.
Cash stripped from extended hours will be used to fund a new patient participation DES to ensure patients are involved in decisions about services.
Clinical DESs for alcohol reduction, learning disabilities and osteoporosis will be extended for a further year. The ethnicity DES has been dropped, but practices must continue to record patient ethnicity and first-language data.
QOF indicators including the access indicators PE7 and PE8 have been dropped to make way for targets to ensure GPs review their referrals, prescribing and local care pathways.
NHS Employers predicted that if GPs can 'mirror' the performance of the top 25% of practices in the way they refer and prescribe, the NHS would save £800 million a year.
But GPC negotiator Dr Chaand Nagpaul assured GPs that their pay would not be linked to specific referral or emergency admissions statistics. The BMA has been critical of plans to pay GP consortia a 'quality premium' based on their ability to stay in budget and achieve outcomes.
Dr David Jenner, GMS/PMS lead at the NHS Alliance, said the new indicators were not in keeping with the original intention of QOF, 'that everything in it must be evidence-based'. But 'at least the money is still in QOF', he said.
Laurence Slavin, a partner at specialist medical accountants Ramsay Brown and Partners, said: 'GPs' expenses are going up. It's not going to be enough to cover rising expenses.'
Dr Jenner said the uplift 'wouldn't even touch the sides' as national insurance contributions rise by 1% in April.
The contract agreement covers England, Scotland and Wales but is still under consideration in Northern Ireland.