"Now that the NCAA has concluded their investigation and penalized the University of Oregon and its football program, I want to apologize to the University of Oregon, all of its current and former players and their fans," Kelly said in the statement. "I accept my share of responsibility for the actions that led to the penalties.
"As I have I stated before, the NCAA investigation and subsequent ruling had no impact on my decision to leave Oregon for Philadelphia. I have also maintained throughout that I had every intention to cooperate with the NCAA's investigation, which I did.
"I do expect the University of Oregon and its football program to continue to thrive at a high level. They are a talented and resilient group of coaches and players, and I'm sure they will attempt to put today's news behind them very quickly and move forward as they prepare for the 2013 season."
The NFL responded with a brief statement regarding Kelly and his role in Oregon's violations.
"We are not familiar with the details at this point and prefer not to comment," a league spokesman said.
An 18-month show-cause order was placed for Kelly in addition to the penalties against Oregon. That requires schools wishing to hire him to appear before the infractions committee to determine if the school should be subject to the show-cause procedures.
While the NFL hasn't taken action against Kelly, NFL coaches and players have been penalized in recent years for their roles in collegiate scandals.
In 2011, former Ohio State coach Jim Tressel was forced to sit out seven games as a replay assistant for the Indianapolis Colts stemming from an NCAA investigation that found Buckeyes players had received improper benefits. The Colts self-imposed that penalty, but former Buckeyes quarterback Terrell Pryor was forced to miss the first five games of the 2011 season by the NFL after having been selected by Oakland in the league's supplemental draft.
Kelly led the Ducks to BCS Bowls in each of his four years at the helm. Oregon finished 12-1 last year, defeating Kansas State in the Fiesta Bowl.
The NCAA has been looking into Oregon's recruiting practices since questions arose over a 2010 payment of $25,000 to Willie Lyles and his Houston-based recruiting service, Complete Scouting Services. Lyles had a connection with an Oregon recruit.
The infractions committee found that Lyles provided cash and free lodging to a prospect, and engaged in impermissible calls and off-campus contact with prospects, their families and high school coaches.
It also said the football program allowed staff members to engage in recruiting activity, exceeding coaching limits.
The NCAA said Kelly was unaware of Lyles' involvement in recruiting, but the committee noted it is the head coach's responsibility to know the rules and ensure staff and coaches comply with them.
Kelly was replaced by offensive coordinator Mark Helfrich, who will make his debut as head coach on Aug. 31.
Oregon was previously penalized by the NCAA in 2004 for a major violation involving the improper recruitment of a junior college player by an assistant coach. The university was put on probation for two years and the unidentified assistant coach was suspended without pay for a week and restricted from some recruiting activities.
The Ducks remained eligible for postseason play and did not lose any scholarships because of that violation, which occurred in 2003.
Contact Mike Still at firstname.lastname@example.org.
This article contains information from the Associated Press.