Comanche sailed into Constitution Dock in Hobart after crossing the finishing line at around 10 p.m. local time (1100 GMT) ahead of compatriot Rambler 88, which was set to take second place, followed by Australia's Ragamuffin 100 and Italy's Maserati.
Rambler 88 had led the race for several hours after Comanche briefly retired on Saturday night, before quickly reversing that decision and electing to battle on.
Most of the leading yachts sustained damage this year, amid wild weather and southerly gusts of up to 40 knots which knocked out the Australian pre-race favourite Wild Oats XI, thwarting its bid to break its record of eight victories.
Organisers say it has been the toughest race since 2004.
It is a sweet victory for Comanche's owner Jim Clark as well as for Australian co-owner Kristy Hinze-Clark, who was among the crew and was showered with champagne as the yacht arrived in Hobart to a crowd of supporters dressed in American Indian headdress.
Even more so for skipper Ken Read.
"That is a hard, hard body of water," Read told reporters after arriving, recounting his decision to continue the race despite damage to a daggerboard and a rudder.
"It was my decision. Sure enough this boat did its thing and got us out of trouble.
"We love this boat."
It is the first victory for Comanche, a 100 foot super-maxi designed to be the fastest monohull ever built, and deliberately made to break records. It is also the first time since 1998 that a U.S. yacht has won the 'blue water' event.
On its first attempt at the 630 nautical mile classic in 2014, Comanche lost its early lead and ultimately had to settle for second place as Wild Oats XI won a record eighth line honours title.
Comanche had already stamped its seal on the race as the fleet headed out of Sydney Harbour on Saturday but then ran into trouble as conditions worsened a few hours later.
Its crew spent 13 hours battling to regain the lead from Rambler 88, which belatedly discovered it too had sustained damage.
Comanche finally crossed the finish line in a time of two days, eight hours, 58 minutes and 30 seconds.
(Reporting by Chris McCall; editing by Amlan Chakraborty)
