There were seven lead changes at GIO Stadium before a late rally from the Brumbies ensured another night of capital returns.
Andy Muirhead's 83rd minute go-ahead try was crucial before Len Ikitau sealed the points, going over with fewer than three minutes remaining to seal a victory the Brumbies almost fumbled.
Stephen Larkham's side looked the business in the first 40, starving the South Islanders of the ball with smart possession rugby.
They led 15-5 lead at the break, boasting three-quarters of the territory and possession in the first half.
However, the men from Otago roared back with two tries in 15 minutes, leading by four and eyeing an away win to kick-start their campaign.
The never-say-die Highlanders even threatened to take the contest to golden point but fell undone in the 84th minute with an error, ending yet another thriller in this superb Super Rugby Pacific season.
"We did well to hold them out at the end but we shouldn't be in that situation," Ikitau told Stan Sport at full-time.
"We switched off (in the second half) but just happy we got the win in a tough game; very physical."
The Brumbies started on the backfoot, losing Corey Toole to the sinbin inside the first 15 seconds with a clunky head clash in the opening tackle from kick-off.
With the numerical advantage, winger Jona Nareki released fellow wideman Caleb Tangitau for the match's opening try.
The Highlanders didn't score again for the half as the Brumbies took control.
Billy Pollard finished a mighty 17-phase move and captain Allan Alaaatoa cashed in after a rolling maul, splitting his ear in the process.
The Highlanders blew a couple of chances to retake the lead, with Sam Gilbert going over but being found to have knocked on earlier in the move, before Thomas Umaga-Jensen coughed up the ball with the try line in sight.
The visiting side had been starved of the ball and looked shaky with it - until they emerged from half-time.
They put on 14 points in 14 minutes to steal the lead, with Gilbert making amends after slick work from Tangitau, before Nareki screamed through the lines to score the game's best try.
Larkham withdrew Rob Valentini, still recovering from a hamstring injury, on the hour mark as the contest steadied for a decisive final quarter.
The Brumbies returned to their patient first-half ways, Toole sidestepping over the line to finish after 13 phases, and they retook the lead at 20-19.
Falling behind again to a Gilbert penalty, the Brumbies made sure the next lead-change was the last, improving their impressive home record to 18 wins from their last 21.
For the Highlanders, it was another case of close but no cigar. All six of their matches have been decided by eight points or less, with losses in four of them.
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