The Wallabies had the benefit of the howling breeze in the second half and dominated field position and possession but, after debutant Mike Harris squared the ledger in the 41st minute, they couldn't find any more points as the Scots dug in deep.
Wallabies five-eighth Berrick Barnes sent a field goal attempt wide with seven minutes to go, and Harris had a chance to break the 6-6 deadlock with a penalty from 48m out in the 75th minute, but could barely get the shot off the ground.
The result is the second boilover in successive season openers for the Wallabies - last year they were embarrassed by minnows Samoa in Sydney.
It was also the second successive defeat to Scotland. Australia were left shellshocked by a last-minute 9-8 loss at Murrayfield in 2009.
Robbie Deans' side now has four days to recover before they face Wales in the first match of a three-game series in Brisbane on Saturday night.
The dire conditions ensured kicking for territory was almost impossible for the Wallabies kickers in the first half.
But overall, Australia were disciplined in defence, and gave Scotland playmaker Laidlaw only three opportunities to make the most of the wind advantage and post points.
Match-winner Laidlaw missed his first penalty attempt in the 16th minute from wide out, but made no mistake with his next two shots - his second goal piloted over from 35m out and five metres in from touch to give the visitors a 6-0 lead.
Harris replied just before halftime to cut the deficit at the break to three points.
A crowd of 20,088 turned out despite the conditions for the first rugby test in Newcastle.
- AAP
