Connor McDavid scored the winner after much-maligned Canadian goalie Jordan Binnington had delivered some clutch saves in Boston on Thursday.
The taut action on the ice mirrored the geopolitical tensions bubbling in North America since US President Donald Trump took office last month.
Trump, who has spoken openly about his desire to absorb America's northern neighbour as its "51st state" and has threatened huge tariffs on Canadian imports, called the US team to offer his support ahead of the contest.
Canadian Prime Minster Justin Trudeau bit back after the game.
"You can't take our country - and you can't take our game," he posted on social media.
Despite the public address announcer requesting respect for both team's national anthems, many US fans booed during the pre-game rendition of O Canada at TD Garden.
Canadian fans had jeered the US national anthem at a game in Montreal on Saturday last week, which the Americans won 3-1.
While the Montreal emotionally charged match-up saw three fights break out in the opening nine seconds, there were fewer skirmishes on Thursday but no shortage of pressure.
"Just to see the reaction, to know what it means to us," McDavid said on the ice when asked what the most gratifying thing about the win was.
"I know it's just a quick tournament and it's not an Olympic gold medal or anything like that, but it means the world to our group as you can see. Everybody battled so hard all week.
"It was special."
The inaugural edition of the tournament also featured Finland and Sweden.
Canada drew first blood when Nathan MacKinnon scored through traffic before Auston Matthews wrapped around goal and Brady Tkachuk jammed home the puck to make it 1-1.
The US took the lead in the second period through Jake Sanderson before Canada's Sam Bennett leveled and a scoreless third period set up a furious five-on-five overtime, where McDavid emerged the hero for Canada.
The tournament, which the NHL presented in lieu of its traditional All-Star game, has been hugely successful with Saturday's game between the US and Canada drawing 10.1 million viewers, according to the NHL.
Thursday's numbers are expected to be even higher, both in terms of viewership and sports betting.
