Jones was long thought to be a one-and-done player and is listed as the fifth pick in this season's NBA Draft, according to NBAdraft.net.
Speculation intensified that Jones would leave after he was suspended for the Big 12 Tournament violations made before he arrived in Waco.
Jones joins Ohio State freshman Jared Sullinger as two top flight big men who are opting to return to college, despite the lure of NBA riches.
With Jones returning, Baylor has a young, but athletic team shaping up for 2011-12. With incoming freshman forward Quincy Miller and guard Deuce Bello joining Jones, the Bears have three potential young NBA players to go along with senior-to-be Quincy Acy.
Besides talent, Baylor could start 6'7 Acy, 6'8 Miller and 6'11 Jones forming one of the taller frontcourts in the country.
For his freshman season, Jones averaged 13.9 points and 7.2 rebounds per game and was selected to the Big 12 All-Freshman Team.