The Crusaders won four of their last five games but missed out on the playoffs for the first time since 2001.
The match in Canberra was the last appearance for flyhalf Dan Carter, who is going to play in France after this year's World Cup, while Richie McCaw is expected to retire at the conclusion of the global tournament.
Carter slotted 17 points with the boot, while flanker Matt Todd became the first forward to score a try in five successive games in Super Rugby to help the Crusaders to a 21-10 halftime lead.
The Brumbies scored all three of their tries from rolling mauls with flankers David Pocock, who left the game late in the first half with concussion, and Jarrad Butler smashing over, while they were also awarded a penalty try despite Butler having the ball under control and crashing over.
Christian Lealiifano slotted three conversions and a penalty for the Brumbies, who had got back to 27-24 with 15 minutes remaining.
Referee Jaco Peyper, however, then gave the Crusaders a penalty try after they got their own rolling maul working with seven minutes remaining.
Original source: Crusaders end era with win