Thomas, who battled injuries throughout his senior season, aggravated an ailing ankle injury early in the week of practice, forcing him to miss the game. He suffered an ankle injury in the Yellow Jackets’ final game of the season, which was four weeks earlier.
Thomas still is expected to play in the Under Armour All-American Game on Jan. 2 in Tampa.
Auburn High’s Rashaan Evans led Alabama defensively and was named his team's most valuable player. He recorded eight tackles, four for loss, a sack and three quarterback hurries. He also returned an interception for a touchdown.
Evan is an uncommitted five-star linebacker/defensive end, who led his team to the Class 6A state finals.
Just this week, Evans talked to college coaches from Alabama, Ole Miss, Auburn and UCLA. He still plans to take his official campus visits and said he likely won't make a decision until well into January.
"UCLA has the edge right now, but it changes every week," Evans said. "That's all I can say. It changes every week."
Mississippi's most valuable player, tight end Sammie Epps of Greenwood, said he remains firmly committed to his college choice. He's going to Ole Miss.
"That's where I'm going to be the next four years," he said.
Epps had seven catches for 125 yards Saturday with a 21-yard touchdown late in the first half, but his most impressive play was early in the fourth quarter.
He made a one-handed grab on a short pass and ran 50 yards to the 8-yard line. It set up a 29-yard field goal by Oxford's Cody Mills that ended the scoring.
"I couldn't score the touchdown because I was thinking, 'How did I catch that ball?'" Epps said. "I admit I made a great play. It was in God's hands."
Mississippi moved into position for a potential go-ahead touchdown on its next possession.
On fourth-and-goal at the Alabama 2, Opelika's Stephen Roberts, an Auburn commitment, broke up a pass intended for Southern Mississippi commit Korey Robertson, also of Greenwood.
The play came with 3:21 remaining and helped secure Alabama's sixth straight All-Star win over Mississippi. Alabama has a 20-7 lead in the series.
"Just to have these bragging rights and beat Mississippi again is great," Evans said. "I definitely had a lot of fun with all these guys this week."
Mississippi quarterback Wyatt Roberts of Louisville, a Jacksonville State commitment, finished 10-of-20 passing for 190 yards and a touchdown.
Alabama's Hayden Moore, a Cincinnati commitment from Clay-Chalkville, was 7-of-13 for 95 yards and two scores, both to Demopolis' Demetrius Kemp. Kemp, a Wake Forest commit, had three catches for 72 yards with TDs of 24 and 33 yards.
Alabama linebacker Tre' Williams, an Auburn commit from St. Paul's, finished with 12 tackles. Louisiana-Lafayette linebacker commit Shareef White of Grenada led Mississippi with eight tackles.
Alabama defensive back Marlon Humphrey of Hoover, one of the nation's top uncommitted senior players, made two tackles, broke up two passes and returned one kickoff for 28 yards.