Earlier in the day Kelly gave his initial reaction since the public announcement.
"It was a very difficult decision for me. It took me so long to make it because the people here are special. The challenge, obviously, is exciting for me, but it's an exciting time, it's a sad time," Kelly said.
"Saying goodbye to people that you love and respected. I wanted to make sure I talked to my players and did it in the right fashion and talked to our staff. I felt like I did."
The 49-year-old Kelly becomes the 21st coach in team history and replaces Andy Reid, who was fired on Dec. 31 after a 4-12 season.
Kelly, who was 46-7 in four years at Oregon, interviewed with the Eagles, Cleveland Browns and Buffalo Bills after leading the fast-flying Ducks to a victory over Kansas State in the Fiesta Bowl. But he opted to remain at Oregon before changing his mind.
The Eagles are known to have interviewed 11 candidates, including two meetings with Seahawks defensive coordinator Gus Bradley. Philadelphia has won just 12 games the last two seasons, after winning the NFC East in 2010.
"Chip Kelly will be an outstanding head coach for the Eagles," owner Jeffrey Lurie said in a statement. "He has a brilliant football mind. He motivates his team with his actions as well as his words. He will be a great leader for us and will bring a fresh energetic approach to our team."
Kelly was thought to be Philadelphia's first choice in a long, exhaustive process that took many twists. The enigmatic Kelly reportedly was close to signing with the Browns after a long interview on Jan. 4. He met with the Eagles for nine hours the next day and the roller coaster ended when he decided to remain at Eugene, Ore.
At the time, it was the second straight year Kelly had entertained overtures from NFL teams only to reject them. He turned down Tampa Bay's job deep into negotiations last season.
The Eagles interviewed two other high-profile college coaches - Penn State's Bill O'Brien and Notre Dame's Brian Kelly. Both of them elected to stay with their schools and Philadelphia issued a statement saying it would continue its search as planned.
"There is no question we spent a considerable amount of time and effort looking at who we thought were the best collegiate candidates for our head coaching job. We did so knowing that there was a remote chance that these coaches would leave their current posts," the team stated on Saturday. "We understood that going into the process, but we wanted to leave no stone unturned while trying to find the best coach for the Philadelphia Eagles. We have no regrets about the effort we made in that direction and we will continue to proceed as planned in our search."
Bradley was thought to be the leading contender, though former Cardinals coach Ken Whisenhunt and former Ravens coach Brian Billick were in the mix.
That all changed when Kelly had a change of heart.
Known as an offensive innovator, the visor-wearing Kelly built Oregon into a national powerhouse. The Ducks went to four straight BCS bowl games - including a bid for the national championship against Auburn two seasons ago - and have won three Pac-12 championships.
Kelly originally went to Oregon in 2007 as offensive coordinator under Mike Bellotti. Before that, he was offensive coordinator at New Hampshire, where he started devising the innovative hurry-up offense the Ducks are known for now.
Oregon finished last season 12-1. The team was ranked No. 1 and appeared headed for another shot at the national championship until a 17-14 overtime loss to Stanford on Nov. 17.
It's unknown whether the possibility of NCAA sanctions based on Oregon's use of recruiting services factored into Kelly's reversal. Kelly indicated in Arizona that he isn't running from anything.
"We've cooperated fully with them," he said. "If they want to talk to us again, we'll continue to cooperate fully. I feel confident in the situation."
Following the bowl, Kelly said he wanted to get the interview process over "quickly." Turns out, it was anything but.
"It's more a fact-finding mission, finding out if it fits or doesn't fit," Kelly said after the Ducks defeated the Wildcats, 35-17. "I've been in one interview in my life for the National Football League, and that was a year ago. I don't really have any preconceived notions about it. I think that's what this deal is all about for me. It's not going to affect us in terms of we're not on the road (recruiting). I'll get an opportunity if people do call, see where they are.
"I want to get it wrapped up quickly and figure out where I'm going to be."
Kelly, who never said if he was leaning one way or another following the bowl, doesn't have any pro coaching experience, but aspects of his up-tempo offense are already being used by some NFL teams, including New England and Washington.
"I said I'll always listen, and that's what I'll do," he said at the time. "I know that people want to talk to me because of our players. The success of our football program has always been about our guys. It's an honor for someone to say they'd want to talk to me about maybe moving on to go coach in the National Football League. But it's because of what those guys do. I'll listen, and we'll see."
The Eagles fired Reid after two forgettable years. A late flurry brought the team to an 8-8 finish last season, but this season, Philadelphia endured an eight-game losing streak, and dropped 11 of its final 12 games. A 3-1 start soon washed away, and Reid's tenure ended not long after.
Oregon's players gave Kelly a Gatorade bath as the final seconds ticked off the clock vs. Kansas State, and afterward a few of the Ducks seemed resigned to their coach moving on.
"We'll have to see," quarterback Marcus Mariota said. "Whatever he decides to do, we're all behind him. He's an unbelievable coach. He's not only a football coach, but he's someone that you can look to and learn a lot of life lessons from. Whatever happens, happens. But we're all behind him.
"We'll see where it takes us."