Both sides were playing purely for pride as they had already been eliminated from contention but Thunder produced a hard-working display to get the win.
Hank Rivers led all scorers with a double-double of 27 points and 13 rebounds, with Lithuanian Tomas Seidukis and Bud Johnston both getting 14 points.
Thunder coach Daniel Hildreth said: “I was very proud of the display tonight, we showed great professionalism and played hard throughout.
“It was also pleasing to see the Thunder juniors all out on the court and playing at senior level. They all worked so hard and it’s a credit to the club’s junior programme that we have got guys that play hard every time they are on the court and that they listen to instructions and constantly thrive to get better.”
Thunder begin the EBL Division 1 season on Saturday when they host Essex Leopards (7.30pm). Worthing then travel to Westminster Warriors in the third round of the National Cup on Sunday.