Jones, 25, 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.
Jared Hicks and Benjamin Cook were also arrested on misdemeanor drug charges. Jones will be arraigned Friday on a charge of felony possession of a controlled substance.
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 Jacksonville thought he could be.
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.