Valerie Sanderson scored her fifth goal of the tournament in the 13th minute and Canada will return to the title match with a chance to defend its crown.
It will face southern neighbor the United States, 7-0 winners over Panama in Thursday's earlier semifinal, for the championship on Saturday. The game will be a rematch of the semifinals from 2010, when Canada prevailed on penalties after a 0-0 draw.
Mexico will have a chance to claim the third CONCACAF berth in the U-17 Women's World Cup in Azerbaijan September 22-October 13 when it plays Panama in the third-place match Saturday.
Canada had the better of play from the start with Clarke getting the first shot, a right-footed drive from 25 meters that went directly into goalkeeper Gabriela Paz.
Mexico was limited to Cynthia Pineda's 30-meter free kick over the bar in the 12th before Canada took the lead.
Clarke turned to hit a drive from 25 meters that Paz extended to her left to block, but Sanderson ran in to pounce on the rebound and tapped it in from the edge of the six.
Canada continued to dominate until the final minutes of the half, but Mexico opened the second half with more energy and had two chances within two minutes. Michelle Gonzalez drove a right-footed shot from 27 meters that Canada keeper Kailen Sheridan had to tip over the bar.
And on the ensuing corner kick by Karla Nieto, Luz Duarte put a header wide from just outside the goalbox.
Mexico continued to generate chances, including Nieto's reaction of Kadeisha Buchanan's attempted clearing header in the 52nd. But Nieto's right-footed shot from outside the area curled wide right.
Canada reclaimed some momentum with shots by second-half substitute Nichelle Prince in the 62nd and Lindsay Agnew in the 64th, and then held on to earn a chance at retaining the title.
For Mexico, it was a second straight loss, having been outscored 4-0 since beating Trinidad and the Bahamas 8-0 over the first two matches.