The quarterback was entering the final year of his deal with the NFC East side, and talks between him and the club appeared to be at an impasse during the off-season.
However, the two parties have now agreed on a deal worth $84m (£54.4m), with $65m ($42.1m) guaranteed, until the end of the 2020 season.
"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.
"Once the talks got going and we were very close, I definitely wanted to try to get it done before the season, so I could just think about football. It's good to have that over with, so I can work on playing football and winning football games."
The Giants face the Dallas Cowboys in their season opener on Sunday.