Updated

Baylor freshman Perry Jones was declared ineligible by the NCAA on Wednesday after an investigation about whether Jones or his family received preferential treatment or improper benefits from an AAU coach before enrolling in college.

The NCAA's decision came only hours before the Bears lost 84-67 to Oklahoma in the first round of the Big 12 Conference tournament. Baylor played without the 6-foot-11 Jones, a starter and one of the nation's top freshmen averaging 13.9 points and 7.2 rebounds.

Baylor immediately appealed to have Jones' eligibility reinstated.

"We are profoundly disappointed in the timing and determination in this matter," Baylor athletic director Ian McCaw said in a release from the school before the game. "This outcome appears to be inconsistent with other recent, widely discussed NCAA decisions."

In an interview during the Big 12 Network television broadcast of the game, McCaw referred to "widely publicized" cases involving Auburn and Ohio State football teams this past season.

A year after making it to an NCAA regional final, the Bears (18-13) won't make it to the NCAA tournament this season. But they are waiting for a likely NIT berth and hope Jones will be eligible to play.

The school's release said Jones had no knowledge of three, 15-day loans between his mother and AAU coach that were provided while Jones was in high school. The loans were repaid in a timely manner, according to interviews conducted by Baylor officials and the NCAA staff.

Jones' AAU coach also paid for the player's travel to a professional preseason football game in San Diego before getting to Baylor, the release said.

Jones, from Duncanville, Texas, was the Bears' highest-rated recruit ever. He could also become their first one-and-done player since he is projected to be one of the top picks in the NBA draft this summer.

McCaw indicated that no Baylor representatives were involved or aware of any preferential treatment between the AAU coach and Jones' family, whose relationship dates to at least the sixth grade. The AD commended Jones "for being cooperative and forthcoming during this unfortunate process."

Baylor's release said the issues that led to Jones' ineligibility are not considered to be an institutional violation of NCAA rules.

That is an important distinction for Baylor, which just last summer completed a five-year NCAA probation period with penalties because of wrongdoing under previous coach Dave Bliss. The program was ravaged in the summer of 2003 by the killing of a player by a teammate, and the aftermath caught Bliss in a tangle of lies and financial misdeeds.

Quincy Acy, who had primarily been the Bears' sixth man, started in Jones' place against Oklahoma and had 21 points with 15 rebounds while playing the entire game. Jones was with the team on the bench in a Baylor warmup suit.

The NCAA ruling against Jones came less than a week after a McLennan County grand jury in Waco, Texas, where Baylor is located, declined to indict Bears senior guard LaceDarius Dunn on a felony assault charge. That effectively ended the case that began last fall with his arrest for allegedly breaking his girlfriend's jaw.

Dunn, the Big 12's leading scorer at 19.8 points per game and the league's career scoring leader, missed Baylor's first three regular season games after being suspended by the school after he turned himself into authorities and was arrested in October.

Auburn won the BCS national championship with quarterback Cam Newton, who was declared ineligible by the school and then reinstated by the NCAA after there was no evidence that the Heisman Trophy winner knew his father was seeking money for his son to sign with Mississippi State, or that the quarterback received anything.

Ohio State quarterback Terrelle Pryor and four teammates were allowed to play in the Sugar Bowl even after being suspended by the NCAA for the first five games of the 2011 season for selling jerseys, championship rings and trophies to a local tattoo parlor owner.