Newton hooked up with Louis Murphy on a TD pass, going 6-of-15 through the air, as the Panthers improved to 2-1 in the pre-season.
Gary Barnidge hauled down scoring strike from Derek Anderson with 11 1/2 minutes to play to provide the winning margin for Carolina.
Mark Sanchez connected on 11-for-18 attempts, amassing 123 yards with an interception for the Jets, who fell to 0-3 in exhibition play.
Tim Tebow also played behind center for New York, completing 4-of-14 passes for 55 yards and an interception.
Tebow also rushed for 45 yards on five carries.