The 25-year-old Jones and two others were arrested early Thursday. A police report said officers approached the car and an officer drew his handgun after Jones did not immediately show his hands.
Police said they searched the vehicle and found a plastic bag filled with a white substance that tested positive for cocaine and a jar with possible marijuana residue.
Jared Hicks and Benjamin Cook were also arrested on misdemeanor drug charges.
Jones was released from the Washington County jail on $2,500 bond. His arraignment on a charge of felony possession of a controlled substance was set for Aug. 11, two days after Jacksonville's preseason opener against Atlanta.
Police said 6 grams of cocaine was found. The threshold for potential charges of possession with intent to deliver is 1 gram. However, prosecutor John Threet said there is no evidence that Jones intended to deal the drug.
Jaguars owner Wayne Weaver said he was waiting to learn details of the case.
"We're trying to investigate that now," Weaver said. "We don't have all the facts. We will comment on that once we have all the facts."
Jones, a star quarterback at Arkansas and a first-round pick in 2005, failed to develop into the go-to receiver for Jacksonville.
Jones caught 77 passes for 1,075 yards and nine touchdowns in his first two pro seasons, but he struggled in 2007.
Last season, coach Jack Del Rio became increasingly frustrated with Jones' demeanor and work ethic, making him inactive for three games. In the offseason, the Jaguars signed free agent Jerry Porter and traded for former first-round pick Troy Williamson.