The Brumbies' 10-game home winning streak was shattered four minutes into injury time when the Highlanders crashed over to snatch a 23-22 win on Saturday.

It was the first time the Brumbies had been beaten in Canberra in 12 months Teariki Ben-Nicholas late try would have been hard to swallow given the circumstances.

The Brumbies were fighting against the odds before the game even started when Irae Simone, Darcy Swain, Bayley Kuenzle and assistant coach Peter Hewat were quarantined.

Medical staff are still trying to work out what the ailment is in the hope it won't spread any further before the next game against the Waikato Chiefs.

It's unknown if Simone, Swain and Kuenzle will be fit to travel with the rest of the team, and the late changes led to 18-year-old Reesjan Pasitoa making his debut as the second youngest player in Brumbies history.

The contagious virus has also hit staff and head coach Dan McKellar. Symptoms appear similar to mumps, but blood tests last week ruled it out as the problem.

McKellar called Pasitoa at 8am on game day to tell him he was about to make his debut and was still tinkering with his plans until after lunch.

Adding to the woes, try-scoring hooker Folau Fainga'a may have suffered an ankle injury and will likely need scans to determine the extent of any damage.

"It's been a tough couple of days for us. Ringing blokes around lunch time ... we spoke about it before the game and I thought we showed a lot of resilience," McKellar said.

"I thought we could be proud of our effort. We're in the middle of getting tests done now. I'd need to talk to the medical staff.

"Any sort of virus, you've got to be really careful in our environment."

Len Ikitau had to play the unfamiliar role of inside centre and Pasitoa was thrown in for the last eight minutes to start his Super Rugby career.

Pasitoa is now the second youngest Brumby, falling one day short of equaling Matt Toomua's record.

The pre-game chaos and thunderstorm appeared the rattle the Brumbies early, misfiring as the Highlanders took the lead.

But Folau Fainga'a scored a hat-trick from the back of the unstoppable rolling maul, taking his season tally to five and putting the Brumbies ahead with time running out.

A Ryan Lonergan penalty stretched the lead to six points, but the Highlanders had one last shot at victory.

The Brumbies tried to shut the game down with 90 seconds left in the hope of hanging on for what would have been a gritty win.

They sucked in defenders before giving away a penalty with 15 seconds left. It was the crack in the door the Highlanders needed and Ben-Nicholas scored three minutes into injury time to deflate the 7270 soaked and dedicated souls.

"We've practised [shutting down the game] and I back that call," McKellar said.

Captain Allan Alaalatoa added: "Our defence was solid all night. Right down to the last try I was confident we could hold them out.

"We just needed to be more clinical at the end."

The Highlanders were lucky to still have 15 men on the field at the end of the game after Patelsio Tomkinson escaped with a yellow card for a shoulder charge.

Tomkinson made contact with Tom Banks' head, which is usually penalised with a red card. The winger instead spent 10 minutes in the sin bin, but will likely be cited for the incident.

"It's a tough one. If you referee it to the letter, it's contact with the head," said Highlanders coach Aaron Mauger.

"I don't think there was any malice there. There was nowhere for him to go, it happened in a split second. I don't think there was any chance of him pulling out."

It was the Brumbies' first loss in Canberra since round one last year and they have now lost their past five matches against the Highlanders.

The Brumbies slowly worked their way into the contest, turning down a penalty shot to go for rolling maul glory and it paid dividends when Fainga'a touched down for a familiar try.

The hooker was at it again before half-time, scoring from the back of another maul to take his try-scoring tally to four for the season.

The Brumbies barely had time to celebrate because Jona Nareki charged down Noah Lolesio's clearing kick after the restart and scored to break the momentum.

It gave the Highlanders a chance to snatch a one-point lead before the break and the gap was four points in the first minutes of the second half.

When the Brumbies finally got in their attacking zone, Fainga'a set up at the back of the maul again to add another try to his growing tally.

He has now scored 17 tries since last year and looks set to be the Brumbies' leading scorer again this season.

Josh Ioane missed a long-range penalty attempt with eight minutes left, which would have locked the score at 19-all.

Lonergan made no mistake at the other end with his long attempt before the Highlanders threw one last wave at the Brumbies.

But lock Murray Douglas was sent to the sin bin for repeated infringements and the Highlanders gathered steam to inflict the Brumbies' first loss of the season.

"I'm very proud and shattered at the same time," McKellar said.

"I thought we were one more carry away from putting the ball into touch and it being a pretty famous six-point win.

"[The Highlanders] were good enough to squeeze out a result there, but I'm really proud of the effort."

AT A GLANCE

OTAGO HIGHLANDERS 23 (Jona Nareki, Teariiki Ben-Nicholas try; Josh Ioane 2 conversions, 3 penalties) defeated ACT BRUMBIES 22 (Folau Fainga'a 3 tries; Ryan Lonergan, Noah Lolesio conversion; Ryan Lonergan penalty) at Canberra Stadium on Saturday night. Referee: Nic Berry. Crowd: 7270.