Mathieu, who was a one-time Heisman Trophy finalist, played cornerback until he was dismissed from the team in August after reportedly failing a drug test. Quarterback Jefferson has been playing in the Canadian Football League.
They were released along with Derrick Bryant, a former backup safety. A fourth former player arrested in the case, Karnell Hatcher, remained in jail.
Police said Mathieu, 20, of New Orleans, and Jefferson, 22, of St. Rose, La., were booked Thursday at the East Baton Rouge Parish Prison on charges of simple possession of marijuana.
Hatcher, 22, of Delray Beach, Fla., was booked with second-offense simple possession of marijuana. Bryant, 22, of Lawrenceville, Ga., was booked with possession of marijuana with intent to distribute.
Jefferson's attorney stressed Thursday that "all individuals are presumed innocent" and said he planned to examine the facts of the case.
Jefferson's father, John Jefferson, told the New Orleans Times-Picayune on Friday that his son is innocent, having arrived at Mathieu's apartment just 10 minutes before police got there.
"He was in the wrong place at the wrong time," John Jefferson told the newspaper. "The lawyer looked at it, and it looks like he didn't have any involvement with it.
"He's upset about it, but live and learn."
Baton Rouge police said the arrests came Thursday after officers responded to a complaint about a man attempting to force his way through a security gate at the apartment complex where Mathieu lives. Before officers arrived, a resident let the man, later identified as Jefferson, into the complex and he was seen going into an apartment.
Police said Mathieu answered the door and officers obtained permission to search after smelling marijuana, leading to the arrests.
Officers found a marijuana grinder, digital scale and 10 bags of high grade marijuana, police said in a news release.
None of those arrested have commented publicly on the case. Neither Mathieu nor Bryant had a listed Baton Rouge area phone number.
Information from The Associated Press was used in this report.