Police said Ellis was found to be in possession of marijuana during the stop and was arrested.
He was charged with possession of marijuana and driving without insurance, the team has confirmed.
Ellis would be enrolled in the league's substance abuse program as a first-time offender. A second offense would result in a four-game suspension.
Ellis will play on Sunday when the Jets are in San Francisco, a team official said Thursday night.
"I apologize to my family, the fans and the organization,'' Ellis said in a statement. "As a captain, I set a poor and selfish example for my teammates as well as all NFL players. Although this is a pending legal matter, I understand that I have to be responsible for my actions.''
Jets general manager Mike Tannenbaum said in a statement that he and coach Eric Mangini both spoke to Ellis about the incident.
"He is disappointed with himself and has apologized for his actions," Tannenbaum said. "Personal conduct is important and an area that we stress to the entire organization. Shaun has been a leader on this team and I am confident that he will handle this in the appropriate fashion. The legal process will run its course and the league will handle this matter."
Ellis has enjoyed a resurgence this season with a team-leading seven sacks, his most in four years. He was the 12th overall pick out of Tennessee in the 2000 draft and has 60½ career sacks.
It's the latest legal incident involving players from the New York-area NFL teams.
Giants wide receiver Plaxico Burress accidentally shot himself in the right thigh at a nightclub last Saturday morning and was charged with illegal weapons possession, a felony that requires a mandatory minimum 3½ years and a maximum of 15 years in prison if convicted. The Giants also fined and suspended Burress for four games, and placed him on the reserve non-football injury list, which means he won't be back for the playoffs.
Giants offensive tackle Kareem McKenzie was charged with drunken driving after a traffic stop on Nov. 14. A Breathalyzer test found McKenzie's blood-alcohol level was above New Jersey's legal limit of 0.08. He wasn't suspended by the team.
