The super maxi, owned and skippered by Anthony Bell, crossed the finish line in Hobart in the early hours of the morning to take four hours, 51 minutes, 52 seconds off the previous mark set by Wild Oats XI four years ago.
Wild Oats XI, which had been chasing a record ninth line honours victory, suffered a broken hydraulic ram and dropped out of the race while leading on Tuesday, leaving Perpetual Loyal clear to sail across the Bass Strait to victory.
Bell said he thought his boat would have had a shot at winning even if Wild Oats XI had not broken down.
"This is one for the true believers," he told reporters in Hobart. "I don't think anyone expected us to do well in this race, the bookies certainly didn't ... we came out of the blocks and we raced one hell of a race. We were brave and stuck to the course."
New Zealand's Volvo 70 Giacomo, owned and skippered by Jim Delegat whose two teenage sons were among the crew, finished second some two hours after Perpetual Loyal, just ahead of Hong Kong's Scallywag in third place.
Bell won line honours on Scallywag, then known as Investec Loyal, in 2011 but failed to finish on Perpetual Loyal in 2014 and 2015.
The multi-millionaire accountant to a string of Australian celebrities said he had no intention of defending the title on the boat next year, however.
"With all my heart, no," Bell said before being thrown into the harbour at Constitution Dock by his crew.
"This boat is a great boat and it needs the next owner, someone to pick it up and jump into it with passion and enthusiasm
"We've got some detailed plans about something new and hot that I'm going to do in sailing."
Covering approximately 630 nautical miles (1170 km) of the Tasman Sea and notoriously treacherous Bass Strait, the annual race is Australia's premier yachting event and among the world's most gruelling.
(Reporting by Nick Mulvenney in Sydney; Editing by Ian Ransom)
