Pliskova, meanwhile, will move on to play sixth-seeded Caroline Wozniacki of Denmark, who ousted 10th-seeded Agnieszka Radwanska of Poland 6-3, 6-1.
Stephens, ranked 934th in the world, gave a good showing in her third tournament after missing 11 months due to a foot injury.
She had a 5-1 lead in the first set, and needed just 30 minutes to win it, and an hour and 24 minutes to take the match.
Wozniacki, 2010 Rogers Cup champion in Montreal, had never before won a match in Toronto before this year but will now be playing for her second Canadian title and first trophy of the season.
Wozniacki was previously 0-6 in her career against reigning World No. 1 players.
Sunday, she'll be back in a final for the sixth time this season, and she'll play the victor of the other semifinal, between world No. 5 Elina Svitolina or No. 2 Simona Halep.
The No. 6 seed, 27, beat unseeded American Sloane Stephens 6-2, 6-3 in the first semifinal on Saturday at the Aviva Centre at York University.
When the action resumed, Svitolina, the world number five from Ukraine, regrouped and forced a decider after claiming the second set in 44 minutes during which both women struggled to hold serve. "I didn't expect this type of day but I'm very happy that I could stay very focused".
Svitolina will go into the final against Wozniacki with plenty of confidence having a 2-0 career record against her.
The remaining two quarters will be decided on Saturday. "She was hitting the ball very hard, very consistently".
The afternoon semifinal was briefly delayed in the second set but it did nothing to hamper Wozniacki's progress. I once I kind of got on a roll, I started serving better.
Pliskova played a more patient game of tennis than she is accustomed to playing, and tried dominating with her power in the rallies. Caroline won 53%, and Karolina 47%, of the 221 total points played between them and also kept her unforced errors count to only fifteen errors for the entire match.