The Czechs took advantage when Bryan Young was sent to the box for hooking midway through the first: Michal Repik fired a pass from the left wing into the crease, where Jan Kovar was waiting for an easy equalizer.
The teams tied at the 2002 Olympics and Canada won in 1994 and 2006.
Canada continued to outshoot the Czechs but could not finish, squandering a two-man advantage late in the second period.
Ice Hockey - Pyeongchang 2018 Winter Olympics - Men's Preliminary Round Match - Canada v Czech Republic - Gangneung Hockey Centre, Gangneung, South Korea - February 17, 2018 - Canadian (in black) and Czech Republic players shake hands after the game. They played the Czechs 2-1. "Like if you give everything you've got, then what happens happens and you move onto the next game and you look for some adjustments and you come back ready".
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"It was one of those bounces that didn't go our way tonight, and hopefully we can get those bounces later in the tournament".
Canada have outscored their opponents 11-2 so far and have the competition's second-highest scoring efficiency at 10.68 percent, just behind Switzerland who topped Group B.
"They just kind of rode me in and the door opened and two guys kind of wedged me in there", said the 37-year-old Lee, who saw the chance to draw a penalty.
Then there was Mat Robinson, perhaps here against the longest of odds considering he's one of just two players on the Canadian roster not to have played in an National Hockey League game.
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Fitting, perhaps, that Saturday's misstep came 20 years after one of the most crushing losses in Canadian Olympic hockey history, the semi-final defeat to the Czechs that also came via the dreaded shootout. "It was the game we expected", he said.
Canada's path to the quarterfinals at the Olympic men's hockey tournament hit a bump - but the Canadians are still all but assured an automatic berth as they wrap up Group A action Sunday against host South Korea.
The Czechs fought back again, levelling inside the first minute of the second period. Defenseman Chris Lee fanned on a bouncing puck to the right of the Canadian net, and Kubalik grabbed it and squeezed it between Scrivens and the post, knotting the game at 1-1. He had, however, won the last five duels and eight of the last 10. Scrivens stopped a pair of shots from Roman Horak and Michal Birner, but couldn't contain the rebounds, and former Carolina Hurricane Michal Jordan snatched the loose puck and went top shelf.
The Canadians upped their physical game in the second period, flooring several Czechs.
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Goaltender Justin Peters, defenceman Karl Stollery and forward Quinton Howden did not dress for Canada with defenceman Stefan Elliott and forward Brandon Kozun drawing in.