Baylor was cited for failure to monitor and placed on three years' probation by the NCAA after an investigation found coaches for the men's and women's basketball teams were involved in making more than 1,200 impermissible phone calls and text messages during a four-year span.
The penalties, announced Wednesday, were reached through a summary disposition process which requires the NCAA, the university and all involved individuals to agree on the facts to proceed.
Baylor had already self-imposed penalties and said it cooperated throughout the process.
A probe found approximately 750 impermissible recruiting text messages and more than 500 recruiting calls not allowed under NCAA rules.
Sanctions were levied against men's coach Scott Drew and women's coach Kim Mulkey for their involvement in the impermissible contact.
Drew will be suspended for the first two games of conference play next season and was given telephone call recruiting restrictions, while Mulkey will not be allowed to participate in off-campus recruiting for the full summer recruiting period in July.
Baylor's penalties also included a public reprimand and censure, recruiting restrictions and scholarship reductions.
The men's team was stripped of one scholarship for both the 2011-12 and 2012-13 seasons, while the women's team lost two scholarships in 2011-12.
A former assistant men's basketball coach who committed unethical conduct when he attempted to coerce two other coaches into providing false information during the probe, was given a one-year show-cause order which prevents him from any recruiting activity.
Drew and Mulkey, along with the assistants involved, acknowledged their roles in the case, and one assistant resigned last year.
The probe began in October 2008 when Brittney Griner, then a senior in high school, and her father reported potentially impermissible contact with members of the Baylor women's basketball staff.
Griner, the consensus player of the year, led Baylor to the first 40-0 record in college basketball history and the women's championship this past season.