Veteran Mortlock was the central figure in a concerted comeback at Carisbrook which put the Australian side ahead 30-19 after a cold start had seen them give up 19 points in the game's first 19 minutes.
Highlanders then rallied with two late tries to lead 31-30 within three minutes of fulltime. But Brumbies flyhalf Christian Leali'ifano calmly potted a dropped goal from 25 meters in the dying seconds to give his team a gripping, bonus-point victory.
"I hit (the winning kick) OK. I've hit them a lot better than that over the years but it did enough to go over," Leali'ifano said.
"You have to feel for the Highlanders. They must have thought they had it won but we'll take it. It's never easy to win down at Carisbrook."
Wallabies centre Mortlock scored the Brumbies' first try as they trailed 19-10 at halftime. He then scored the first try of the second half and provided the pinpoint pass which created a fourth, bonus-point try after 52 minutes for Australian teammate Mark Gerrard.
Adam Ashley-Cooper also scored during a Brumbies streak of four tries and 20 unanswered points, bringing his personal tally for the match to 15 points with two conversions and two penalties.
The Brumbies lead peaked with that try and they went scoreless for 28 minutes as the Highlanders, finding a second wind, mounted their own steady comeback.
Replacement prop Chris King scored the home team's fourth try after 72 minutes and Jason Rutledge added another in the 77th minute to give the Highlanders a 31-30 lead. The New Zealanders picked up two bonus points - for scoring four tries and for losing by fewer than seven points.
The Brumbies, reduced to 14 men with the sin-binning of captain Stephen Hoiles, kept their composure under Mortlock's leadership and set a ruck in front of Otago's post from which Leali'ifano dropped the winning goal.
"The way the Highlanders started was definitely a shock," Leali'ifano said. "We had to go back, regroup and try to regain some momentum, which we did."
The Brumbies, lacking intensity from the kickoff, were slow to react on defense and conceded early tries to Highlanders backs Jason Shoemark, Fetu'u Vainikolo and Daniel Bowden. Bowden converted two of those tries to build the home team's early margin.
The Highlanders lost both captain Jimmy Cowan and vice-captain Jamie McIntosh to injuries before halftime and lost their way without the leadership of the two All Blacks.
"We're a young side and losing leadership was a big blow," said Shoemark, who ended the game as captain. "In the second half we went to sleep but the guys come back and we can take some positives from that."
ScorecardScorers:
Highlanders:
Tries: Jason Shoemark, Fetu'u Vainikolo, Daniel Bowden, Jason Rutledge, Chris King
Conversions: Bowden (3)
Brumbies:
Tries: Stirling Mortlock (2), Adam Ashley-Cooper, Mark Gerrard
Conversions: Gerrard (2)
Penalties: Gerrard
Dropped goal: Christian Lealiifano