Mike Williams, who came off the bench to lead Rutgers with 23 points, scored five points during the decisive run after the Blue Devils had rallied to retake the lead.
The Scarlet Knights turned a two-point deficit into a 61-48 lead with 5:17 to go.
The Blue Devils, who lost to Rutgers 79-37 a year ago, refused to go away this time.
Rutgers went up 44-36 early in the second half, but Central Connecticut responded with 10 straight points to take a two-point lead with 10:27 to play.
Deshawn Freeman scored 11 points and seven rebounds, and Eugene Omoruyi had 13 points and seven rebounds for the Scarlet Knights, who got 38 points from their bench.
Tyler Khol scored 22 points, and Mustafa Jones added 14 to lead Central Connecticut.
The Blue Devils played without coach Donyell Marshall and assistant Anthony Anderson, both of whom were suspended for the first two games in what school officials called a "personal matter."
Central Connecticut State jumped out to a 10-2 lead, and Rutgers did not lead until a Williams jumper put the Scarlet Knights ahead 24-23 with 3:26 to go in the first half.
The Blue Devils shot 52 percent from the field in the first half, while Rutgers managed just 30.3 percent. The Scarlet Knights helped themselves with 12 offensive rebounds and led 30-29 at the break.