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With nine minutes remaining, Highlanders winger Fetu'u Vainikolo was ankle tapped by No 8 Stephen Hoiles with the line at his mercy after an exciting bust.
From the resulting penalty, Highlanders fullback James Wilson missed a kickable penalty and the Brumbies were able to hold on to their slender margin.
The inexperienced, injury-ravaged hosts scored three tries to two, including a questionable penalty try, and led 17-7 at halftime to pick up their first win of the competition.
The Highlanders finished easily the stronger team with a breeze at their back, getting right back into the game when reserve prop Chris King was driven over with 15min remaining.
It typified the fine driving play of their pack, led by No 8 Steven Setephano and prop Jamie Mackintosh.
But ultimately it was another unfortunate result on Australian soil for the under-rated Highlanders, who suffered an unlucky six-point opening loss to the Queensland Reds in Brisbane last weekend.
They opened the scoring through a Vainikolo try after a neat bust from first five-eighth Daniel Bowden.
The Brumbies replied quickly through second five-eighth Anthony Faingaa, with fullback Julian Huxley landing the conversion and a penalty.
A penalty try ruling from Australian touch judge James Scholtens in the 28th minute was questionable, having ruled that Highlanders lock Hayden Triggs had tackled Huia Edmonds high and therefore prevented a try.
The tackle by Triggs, who was also sent to the sinbin, didn't appear illegal although it appeared Edmonds may have scored anyway -- if further out from the posts.
Two Wilson penalties closed the margin to 17-13 early in the second half but the Brumbies' crucial only score in the second half then went to Hoiles, who carried two tacklers over the line.
The Highlanders created no shortage of chances but a break after the final hooter by centre Niva Ta'auso was foiled by a subsequent knock on.
The Highlanders will host their first home match next weekend, against the New South Waratahs.
Highlanders captain Jason Macdonald was disappointed to again get so close.
"I thought If we had a get out of jail free card that we might have been able to use it tonight, but it wasn't to be," Macdonald told Fox Sports.
"The Brumbies capitalised on the mistakes that we made, and we made a lot of them.
"When we hold onto the ball we play a good brand of footy but we've got some areas of our game that we need to fix up. Ball retention seems to be one of them at the moment."
Brumbies skipper George Smith was pleased with the improvement from last weekend's heavy opening loss to the Crusaders.
"To get a win at home is fantastic for the boys, we really stuck at it for the last 20 minutes," he said.
Result of the Super 14 rugby match at Canberra Stadium tonight.
ACT Brumbies 22 (Anthony Faingaa, Stephen Hoiles tries, penalty try; Julian Huxley pen, 2 con) Highlanders 20 (Fetu'u Vainikolo, Chris King tries; James Wilson 2 pen, 2 con). Halftime: 17-7.
Brumbies: Julian Huxley, Mark Gerrard, Tyrone Smith, Anthony Faingaa, Francis Fainifo, Christian Lealiifano, Josh Holmes; Stephen Hoiles, George Smith (captain), Mitch Chapman, Al Campbell, Mark Chisholm, Guy Shepherdson, Huia Edmonds, Nic Henderson. Reserves: Saia Faingaa, Salesi Maafu, Peter Kimlin, Julian Salvi, Patrick Phibbs, Peter Playford, Afusipa Taumoepeau.
Highlanders: James Wilson, Paul Williams, Niva Ta'auso, Johnny Leota, Fetu'u Vainikolo, Daniel Bowden, Jimmy Cowan, Steven Setephano/Ezra Taylor, Alando Soakai, Adam Thomson, Tom Donnelly, Hayden Triggs, Clint Newland, Jason Macdonald (captain), Jamie Mackintosh.
Reserves: David Hall, Chris King, Isaac Ross, Tim Boys/Ezra Taylor, Toby Morland, Mike Delany, Brett Mather.
