They also selected Clemson defensive tackle Dexter Lawrence 17th overall and traded into the bottom of the first round to take Georgia cornerback Deandre Baker at No. 30.
The Giants selected Jones ahead of highly regarded outside linebacker Josh Allen, a move that wasn't particularly well received. Fans at the team's draft party booed. Allen was selected by the Jacksonville Jaguarswith the next pick.
Giants general manager Dave Gettleman didn't want to wait until the 17th pick to grab his future franchise quarterback, saying he was afraid Jones would not have been available.
"You never know," Gettleman said. "I was not willing to risk it."
Asked what he'd say to fans who booed the Jones pick, Gettleman said, "In time, you'll be very pleased."
In the meantime, the Giants will have Jones sitting behind Manning, the two-time Super Bowl MVP who is 38 and entering the final year of his contract.
Gettleman called Manning while they were selecting Jones. He reiterated that Manning is expected to remain the starter this season.
"The goal is for Eli to be our quarterback," Gettleman said.
Coach Pat Shurmur added that he told Manning, "It's your job to win games and keep this guy off the field."
It's unclear when the passing of the torch will occur. Despite the significant draft capital spent on Jones, it's hardly a certainty that he will be the quarterback in 2020.
"Absolutely not," Gettleman said. "Maybe we're going to be the Green Bay model, where [Aaron] Rodgers sat for three years. Who knows? It's one of those deals where it doesn't make a difference what position it is. You can never have too many good players at one position."
When asked if it is possible that the No. 6 overall pick might sit for three years, Gettleman didn't budge.
"Who knows?" he said. "I might go out to my car and get hit. ... You don't know. We drafted a quarterback that we believe is a franchise quarterback."
Manning is now a lame duck quarterback in the present. Gettleman called it a hypothetical when asked if there would be talk of a contract extension.
The Giants had the same grades on Jones and Allen. Gettleman said they were on the same line. In this case, the quarterback position won.
"It's a wonderful thing when need and value match," Gettleman said. "We're thrilled to get Daniel. He was up there with everybody else on our board in terms of value. He is just perfect for us. We really believe in this kid. We really believe he's gonna be a nice -- not a nice -- a real quality quarterback for us, for our franchise."
The 6-foot-5, 221-pound Jones has a connection to Manning through Duke coach David Cutcliffe, who coached both Eli and Peyton Manning in college and remains tight with the brothers. Jones has developed a relationship with Eli and Peyton through Cutcliffe and has attended the Manning Passing Academy multiple times.
Cutcliffe and Jones watched film of the Manning brothers and talked about their development.
"Just hearing those stories and learning from some of those experiences was an awesome perspective for me and certainly a great situation,'' Jones said.
Jones threw for 2,674 yards with 22 touchdowns and nine interceptions as a junior this past season. He rushed for 319 yards and three touchdowns.
Gettleman admittedly fell in love with Jones' tape. It was at the Senior Bowl that the deal was sealed, as Gettleman was convinced after seeing Jones play three series. He saw "a professional" and said that was the point that it was "full-bloom love."
Jones became the third straight Senior Bowl MVP drafted by the Giants, joining Davis Webb and Kyle Lauletta.
There was a range of opinions on Jones leading up to the draft. ESPN draft analyst Mel Kiper Jr. had him ranked 23rd on his list of top 300 prospects. ESPN's Todd McShay was less enamored by Jones' skills and had him 59th.
One NFL scout said Jones is a "pedestrian talent" and "backup." One coach who watched his tape saw a "fairly high ceiling" and asked, "What box doesn't he check?"
"Physically, I think I can make every throw on the field,'' said Jones, who noted that he was not sure when he would be taken until the Giants called him before announcing the selection. "My accuracy is a strength of mine, and I have the athleticism to extend plays. I play outside the pocket if I need to. Physically, I can do both those things well.''
The Giants hosted Jones for a predraft visit, and Shurmur visited him at Duke. He came away impressed. The Giants raved about his makeup and toughness.
While Jones is the centerpiece, this will go down as a historic first round for the Giants. It was the first time the team had three picks in the first round.
Lawrence had 7.5 tackles for loss for the Tigers last season, when he was one of the best run defenders in the country. He tested positive for ostarine in NCAA drug testing and missed Clemson's 44-16 victory over Alabama in the College Football Playoff national championship in January.
The Giants considered Baker the best cover cornerback in the draft. They traded pick No. 37, a fourth-rounder (132) and a fifth-rounder (142) to the Seattle Seahawks to land the Georgia cornerback.
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