It was his second straight victory after saluting at the same track on Melbourne Cup Day almost two weeks ago.
"It's been a long road with this horse. He's had a lot of injuries and it looked like being the best horse I ever trained, but unfortunately he had a few injuries and it's taken a lot of work to get him back to the races," Pepper said.
"It's great to see him win two in a row, it's huge. It's been a great team effort ... I'm bewildered by it actually."
The Joe Cleary-trained Bart jumped out of the barriers to the early lead, where he stayed until the home turn as Appoint Percy took over.
The son of Sir Percy held on to win by half-a-length from Danny Williams' Laughing Or Crying, with Just Dylan another length away in third.