The NCAA already hit both schools with a postseason ban because of low APR scores, which were released last month. But the SWAC championship did not apply because the NCAA considers the game an extension of the regular season.
The league does not receive an automatic bid to the Football Championship Subdivision playoffs.
A message was left seeking comment from SWAC commissioner Duer Sharp.
Jackson State president Carolyn Meyers called the SWAC's decision "regrettable" in a statement released by the university.
"JSU is disappointed in the decision of the SWAC to uphold the NCAA ban on postseason play due to our low APR," Meyers said.
"We remain committed to the timely graduation of all our students -- student-athletes included."
The problems with APR scores have been widespread for schools in the SWAC and MEAC, which are completely comprised of historically black colleges and universities. The two leagues account for only 24 of more than 340 schools evaluated by the NCAA, but out of the 58 harshest penalties handed out by the NCAA in May, half of them went to teams in the two conferences.
The schools in both leagues typically don't have large athletic budgets, and lack the athletic infrastructure of BCS schools that employ well-staffed compliance departments and sprawling academic centers for athletes.
Southern is the first NCAA program banned from the football and basketball postseasons because of low APR scores.
The SWAC's decision is sure to put a damper on the upcoming football season. Southern and Jackson State have two of the league's most storied histories and most passionate fan bases. The two schools have combined for more than 30 league championships, and the annual game between the two rivals can draw up to 40,000 fans.
Southern last won the league title in 2003. Jackson State's last title was in 2007.
The SWAC released a statement Thursday saying any future NCAA postseason bans also would prohibit teams from playing in league championships.