The NCAA invoked the punishment after finding the university allowed 129 student-athletes in 13 sports during seven academic years to compete and receive financial aid and travel expenses when they were ineligible.
The basketball Tigers, banned from post-season play this coming season, gave up all their wins from 2006-2007 through 2009-10, lost two scholarships for the next three years, and will be under recruiting restrictions for two years.
Tony Harvey, who resigned as the men's basketball coach after last season, was cited by the NCAA for unethical conduct for providing false or misleading information during the organization's investigation. He was issued a three-year, show-cause order.
The Tigers football program will be under a post-season ban in 2013 and 2014, along with scholarship cuts for four years.
The NCAA found former Coach Johnnie Cole "knowingly allowed a booster to recruit" for the program.
The NCAA also said Harvey and Cole sought to place two student-athletes under football scholarships to circumvent previous basketball limits.
The NCAA Infractions Committee noted Texas Southern has either been on probation or had violations for 16 of the past 20 years.
In a wide-ranging decision, the NCAA also cited the school for lack of institutional control of its athletics program, allowing boosters' involvement in recruiting, academic improprieties and exceeding scholarship limits.