The deal is worth $84 million, including $65 million in guaranteed money, sources told ESPN's Chris Mortensen.
The Giants, according to the sources, agreed to include a no-trade clause in Manning's new deal, which had been a major hurdle in the talks.
"I'm obviously excited knowing I'll be a Giant for a long time," Manning said in a statement. "This is where I got started and where I want to finish. I still have the same mentality. My goal is to earn this contract and do my best and keep trying to win championships for the Giants.
"Not many people come to a team and play there for an extended period of time or, hopefully, their whole careers. I feel obviously blessed to be part of the Giants family and to have played my career here, with the fans, the ownership and everything the Giants represent. It's been a great 11 years going into 12, and hopefully we can continue to have some great years, and there are a lot of fond memories ahead of us."
ESPN's Dan Graziano reports the deal includes a $31 million signing bonus and will pay Manning $68.5 million over the first three years.
Manning's $21 million average in new money on the extension will rank him fourth among quarterbacks in the NFL, behind Aaron Rodgers ($22 million), Russell Wilson ($21.9 million) and Ben Roethlisberger ($21.85 million).
"I'm glad we were able to get this done so we all can focus on winning football games," Giants general manager Jerry Reese said.
Manning was entering the final year of his contract. He and the team had said they were comfortable playing out the year and doing the extension next spring or summer, but both sides preferred to have it done before the season.
"I think that there'd be no doubt that for all of us to have that behind us, particularly Eli and his family to have that behind them and to no longer have the questions about that every day, I think that's a good thing," Giants head coach Tom Coughlin said Friday.
"He's our quarterback, he's the guy that's our leader and he's been the MVP of two Super Bowls," Coughlin said. "He's a great player and we are excited to have this behind us and accomplished, and we look forward to having him on the field."
The Giants play the Dallas Cowboys in their season opener Sunday night.
Information from ESPN Giants reporter Dan Graziano was used in this report.