Wild Oats smashed the race record when it crossed the line at Constitution Dock in Hobart at 9.48 pm (1048 GMT) on Wednesday after taking one day, eight hours, 48 minutes and 50 seconds to complete the 630-nautical mile (1,170 km) race.
Comanche, which had led for much of the race before both boats stalled in fickle winds on the River Derwent, finished just over 26 minutes later.
Comanche, however, had protested about a near collision between the two super-maxis when Wild Oats completed a tack about 15 minutes after the start in Sydney harbour.
The jury upheld the protest on Thursday and imposed a one-hour penalty on the Mark Richards-skippered Wild Oats, which had won the race eight times before.
"Wild Oats XI had to keep clear, failed to keep clear while tacking, Oats did not do turn," race organisers said.
"Decision is penalised by one hour. Comanche is line honours winner."
It was the first time a yacht had been stripped of line honours since Rothmans in 1990.
"I didn't expect to protest in order to win the race, it was all about our actions to avoid a collision and the fact that was necessary," Comanche owner Jim Cooney said.
"I feel the rules are there to protect people's lives and if we can't rely on that then there is a difficulty in the sport.
"It's a great relief that all the effort of the crew the support crew and my family was vindicated, so it was a relief that we did deserve the win."
Richards had told reporters earlier on Thursday he would have taken a 720-degree turn penalty at the time of the incident if they thought they were in the wrong.
"Everyone is a genius in hindsight," Richards said after the decision when asked if he regretted not taking the turn penalty at the time. "We had spoken about ... but that was the decision we made and you have to live with it."
Five boats in total, also including Black Jack, InfoTrack and Beau Geste, beat the previous record of one day, 13 hours, 31 minutes and 20 seconds.
(Reporting by Greg Stutchbury in Wellington; Editing by Nick Mulvenney)
