Flanker Liam Messam and replacement back Robbie Robinson scored tries four minutes apart deep in the second half and fly-half Aaron Cruden added 17 points with his boot to rescue the home side from a potential upset.
The Brumbies, trying to become the first team to win the title having played their semi-final on another continent, had led 22-12 in the 65th minute courtesy of a converted try and five penalties from centre Christian Lealiifano.
The Chiefs are the fourth team to win back-to-back titles and join the Auckland Blues, Canterbury Crusaders, Bulls and Brumbies as multiple winners of the southern hemisphere's annual provincial competition.
"I think it was a real tough final," said Chiefs co-captain Craig Clarke, one of string of senior players moving on at the end of the season.
"We have to pay credit to an awesome Brumbies team for a hell of a performance, especially after all the travelling they've done.
"It's been an awesome couple of seasons and a great group to be part of. Big ups for what we have done."
For much of the evening, though, it looked like the Canberra-based Brumbies might just become the first foreign team to win the title on New Zealand soil.
Kicking for territory and targeting the breakdown, the visitors raced out to a 9-0 lead in the first 20 minutes on the back of three Lealiifano penalties.
The hosts, though, got over their slow start and started to ramp up their attack with Cruden punishing the Brumbies for their increasingly regular infractions in the tackle area.
Cruden missed his first attempt at goal but nailed the next three to draw the teams level at 9-9 after 32 minutes and it looked like the Chiefs would take the momentum into the break.
But three minutes later, home scrum-half Tawera Kerr-Barlow, under pressure from George Smith, threw a pass over the head of hooker Hika Elliot and Lealiifano pounced, racing 40 metres to touch down in the corner with Cruden trailing in his wake.
The Wallabies centre converted his own try to give the Australians a 16-9 halftime lead and, when lock Scott Fardy won a penalty in front of the posts five minutes after the restart, extended it to a 10-point cushion.
Cruden chipped three points off the lead after 48 minutes but he hit the post with his next penalty attempt and the Brumbies stormed back.
Lealiifano put through a grubber kick which winger Clyde Rathbone somehow latched onto to take the ball to the Chiefs' line with lock Sam Carter just failing to convince the TV review official that he had forced the ball down over the line.
A fifth Lealiifano penalty just before the hour mark gave the visitors a 22-12 lead but man of the match Messam signalled the late resurgence when he closed the gap with the Chiefs' first try, coming off a five-metre scrum to crash over the line.
The next score came four minutes later and was the best of the night with the Chiefs taking the ball from deep in their own half to the 22 metre line before Robinson cut through the defence and raced to the line to touch down.
Cruden had missed his first conversion attempt but nailed the second to put the home side in front at 24-22, a lead he extended with his fifth and final penalty seven minutes from time.
The Brumbies' desperation trumped the fatigue of their 23,000-km odyssey to South Africa and back for their semi-final victory over the Bulls and they hammered away at the home side's defence in the dying minutes.
It was to be in vain, though, and the cowbells of the locals rang around the Waikato Stadium in triumph for the second year in a row.
"We led from the start and for them to come from behind speaks loads for this Chiefs team," Brumbies skipper Ben Mowen said.
"They are an outstanding champion side and thoroughly deserve this title. Congratulations on what they have built here in the last two years. It's what we aspire to."
- Sports & Recreation
- Aaron Cruden
- Christian Lealiifano