Jones was charged Tuesday with possession of marijuana second degree and released on $1,000 bond, Tuscaloosa police said in a news release.
Crimson Tide coach Nick Saban released a statement later in the day saying Jones "was given an opportunity academically and from a team rules standpoint, but he failed to do any of the things necessary to comply with the rules of the Alabama football program.
"He was dismissed from the team when he refused to follow the parameters given to him for reinstatement," Saban said.
Saban had suspended Jones indefinitely on Feb. 10 "for conduct not to the standard of the Alabama football program." Safety Geno Smith and since-dismissed defensive lineman Jonathan Taylor were arrested on Saturday.
Smith was arrested on a charge of driving under the influence of alcohol for the second time in his Alabama career. Taylor, who had been dismissed from the Georgia team in July following a domestic violence arrest, now faces similar charges stemming from a separate incident in Tuscaloosa.
Saban steadfastly defended the January signing of Taylor, which had already drawn criticism, on Monday night.
"We've created many opportunities for players through the years and sometimes those things have worked out extremely well," he said. "We're sad to say in this case it didn't and we all take responsibility for that. We have a good program here at Alabama, and we have a lot of good players who have done a lot of good things in this community on our team."
Police say Jones and 25-year-old Brandon Lee Hansberry were arrested after an officer stopped a white Dodge Challenger for speeding at 11:27 a.m. Monday.
The officer smelled marijuana and found the drug and digital scales inside the vehicle, which belonged to Hansberry, according to the police news release. A small amount of marijuana was found in Jones's pocket. Jones ran for 224 yards and two touchdowns as a redshirt freshman last season.
Two other passengers in the vehicle were released without being charged.
Hansberry was charged with one count of marijuana possession first degree and one count of possession of drug paraphernalia. He had an outstanding charge from Tuscaloosa police and was sent to the Tuscaloosa County Jail on $20,000 bond.
Information from The Associated Press was used in this report.