After three long years of sometimes acrimonious contract talks, with the Berkshire Hathaway-owned fractional jet ownership company, the pilots have hammered out a new five-year contract that will pay them a total of $645 million more than Buffett first offered them, The Post has learned.The pilots’ union is expected to announced the new labor deal on Saturday.The annual pay increase is about $115 million, sources said — or $575 million over five years. Plus, the pilots will receive a one-time bonus of $70 million, a source familiar with the numbers told The Post. Buffett, claiming the flyboys were well paid, unsuccessfully pushed for a pay cut, sources said — and for the pilots to contribute to their health care benefits.Buffett told Fox Business Network in May that the pilots were “doing well, and we’re doing well. What we pay is higher than most of our competitors.”Under the new deal, a NetJets captain with 10 years of experience will see a salary jump of 20 percent, to $143,105, the source said. Salaries will rise 2 percent in year four, and 3 percent in the fifth year.Pilots were asking for a 35 percent raise over three to five years.The pilots’ salaries will be within range of those at legacy airlines Delta, American and United.NetJets, the No. 1 shared corporate aircraft company in the US — with a fleet of 700 Gulfstreams and Cessnas and roughly 8,000 well-heeled customers who pay for a set number of hours aboard a private jet each year — has seen demand increase in recent years, putting the union in a better bargaining position.For the pilots, the key to reaching a deal was changing leadership last year at the NetJets Association of Shared Aircraft Pilots Union and becoming much more aggressive, the source said.“We brought the fight to [former CEO] Jordan Hansell and Buffett,” the source added.The NetJets pilots, knowing where Buffett was flying, had picketing pilots waiting for him after many of his trips. They were also effective at getting attention in media, including taking out full-page Wall Street Journal advertisements.Berkshire Hathaway and the pilots union did not return calls.