The NCAA was unable to come to an agreement with Oregon on sanctions over recruiting violations by the football program under former coach Chip Kelly, so the issue was sent to the organization's infractions committee.
The committee's penalties ended up falling mostly in line with what Oregon had proposed earlier.
Oregon will lose a scholarship in each season during a three-year probation period, but avoided a bowl ban and other major penalties under sanctions issued by the NCAA's Division I Committee on Infractions on Wednesday.
The committee also placed an 18-month show-cause order on Kelly, a sanction that will likely have limited impact since he's now coaching the Philadelphia Eagles.
For what was considered major recruiting violations, the outcome was about as good as Oregon could have expected.
"Throughout this process, there has been speculation and innuendo regarding the nature and severity of potential violations, much of which was unfounded," Oregon athletic director Rob Mullens said in a statement. "As stated by the NCAA Enforcement Staff, the violations committed in this case were unintentional."
Oregon lost one scholarship for the 2012-13 academic year and will lose another in 2013-14 under self-imposed sanctions. It also will have its total number of scholarships reduced by one from a maximum of 85 each of the next three seasons, also self-imposed.
The NCAA cut Oregon's official paid visits from 56 to 37 for the next three academic years, reduced its evaluation days for each of the next three seasons and banned the program from using recruiting services during the probation period. Oregon must also disassociate itself from Willie Lyles' Houston-based recruiting service, which was at the center of the investigation.
The show-cause order for Kelly will require schools to go before the infractions committee should they wish to hire him. Former assistant director of operations Josh Gibson was given a one-year show-cause order after the NCAA said he was aware of Lyles' involvement in recruiting and routinely told him to tell recruits to contact football coaches.
"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 a 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."
The NCAA had been looking into Oregon's recruiting practices since questions arose over a 2010 payment of $25,000 to Lyles and his recruiting service, Complete Scouting Services. Lyles had a connection with Lache Seastrunk, a star prep running back from Texas who committed to Oregon in 2010, a month before the payment.
When Oregon later released the recruiting package it said Lyles had prepared for the school, the material was largely outdated. While use of services to identify potential recruits is allowed under NCAA rules, questions were raised about Lyles' relationship with Seastrunk and other athletes from Texas, and whether he steered any prospects to the Ducks, which would be a violation.
Seastrunk redshirted for the Ducks his freshman year before transferring to Baylor prior to the 2011 season.
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 exceeded coaching limits by allowing staff members to engage in recruiting activity.
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.
"I've not met an institution that wants to go through the infractions and enforcement process," infractions committee member Gregory Sankey said. "This was a multi-year effort that certainly existed and there are penalties that impacted the program. The committee made its decisions based on information given to it, not on other speculation and evaluations."
Under Kelly, the Ducks appeared in four straight BCS bowl games including a bid for the national championship against Auburn in 2011. Oregon finished 12-1 last season, capped by a victory over Kansas State in the Fiesta Bowl.
He 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.
AP Sports Writers Anne Peterson in Portland, Ore., and Dan Gelston in Philadelphia contributed to this report.