The Magic lost their 10th in a row in a meeting of the bottom two teams in the Southeast Division.
Jefferson has indicated during the past week that he will likely need ankle surgery after the season and that announcement has coincided with his best stretch of basketball this year.
He scored a season-high 35 points against New York Tuesday and he made 13-of-17 shots against Orlando.
Kemba Walker had 19 points and 10 assists, while both Josh McRoberts and Gerald Henderson scored 17 points. The Bobcats shot 52 percent from the field to win for the second time in three games after a stretch in which they lost eight out of nine.
Arron Afflalo had 24 points for Orlando, which last won Dec. 29 against Atlanta. The Magic became the second team in the NBA with 30 losses this season, joining Milwaukee.