Bruff surprised Wanderers in last year's final and they got a taste of their own medecine at Donnybrook as tries from Niall Malone, Adam Telford and Owen McMurray, who kicked 12 points, and Kenny Morton inspired the Belfast men to victory.
Speaking afterwards, Bruff coach Eugene Murnane said: "Bruff RFC have a wonderful set-up and the work ethic of the squad is second to none. We went 15 games unbeaten in the league so obviously we are disappointed to lose this final.
"Full credit to Instonians though. They put it up to us but this was a game that we wanted to win.
"We will be in Division Two next season, but I won't be with the club for that campaign," added the Welshman, who had three enjoyable years with the Kilballyowen Park outfit.
Garryowen flanker Peter Malone will return next season to Bruff, the club he won an All-Ireland Under-18 title with, as their player-coach.