The construction unions Unite and GMB had been preparing for strike action since members voted last month to reject the previous offer.
The client EDF and the main contractor BYLOR (Bouygues TP / Laing O’Rourke joint venture) then proposed a revised offer, the unions said.
Under the revised offer workers will be paid up to 36% more than the minimum pay rates agreed by the Construction Industry Joint Council. By incorporating a large amount of the previous bonus payments into the basic rate, workers will see holiday pay, overtime rates and pension contributions increase.
Workers will also receive back pay from the period between 1st January 2017 and 31st May 2017, when the interim bonus scheme was introduced.
The dispute had been rumbling since the spring and concerned the pay of workers on the civil engineering side of the project.
Unite regional secretary Peter Hughes said: “This is a landmark agreement which will now set the benchmark for pay rates on flagship construction projects throughout the UK.
“The pay rates agreed at Hinkley Point will provide a significant boost to the local economy and, together with the ambitious apprenticeship programme on the project, will generate much needed skills boost and investment in the south west region.
“The determination of EDF to broker a deal was critical in ensuring the pay negotiations were satisfactorily resolved.”
Unite’s lead convenor at Hinkley Point, Malcolm Davies, said: “The negotiations have been protracted but the unity of the workers on the project has ensured that we have finally arrived at a pay deal which properly financially rewards the workforce.
“Unite will continue to ensure that workers at Hinkley are treated fairly and decently and hopefully we are now entering a period of industrial harmony.”
GMB national officer Phil Whitehurst added: "GMB members have voted, in a very positive and responsible manner, to accept EDF's final offer. The employers’ side in the negotiation should have declared their hand way before January 2017, but chose to take it to the wire.
“This could have resulted in a trade dispute which would have had devastating consequences to this prestigious project. Let's now hope that an open and transparent relationship will precipitate from this on the civil construction phase of HPC."