The 25-year-old Czech, who had a first-round bye, extended her winning streak over the 19th-ranked player to five matches. She earned the No. 1 ranking when Johanna Konta beat Romania's Simona Halep in the quarterfinals at Wimbledon.
"I had a little bit [of nerves] before my match because I really wanted to win this one," Pliskova said. "Also, I knew I have a good record against her. So I just knew if I play solid and OK, I can win it."
Halep, now ranked second and the defending Rogers Cup champion, played the late match against Slovakia's Magdalena Rybarikova.
In other second-round play, ninth seed Venus Williams earned her second career win in Toronto, a 7-5, 7-5 victory over Katerina Siniakova. Williams, the runner-up at the Australian Open and Wimbledon this year, hadn't won in the Canadian city until she beat Irina-Camelia Begu in the first round on Monday.
"It was well-earned. I had to wait a long time for win No. 2," Williams said. "So I would like to build on that to win No. 3."
Pliskova, who broke Pavlyuchenkova seven times over the 72-minute match, said that being the top player in the world didn't make her feel any different before it started.
"I was not really thinking about this," she said.
"I think some moments [of the match] were OK, but otherwise the serve was not great and overall I was not real happy with my game today. But it was enough and so another chance tomorrow to improve."
In another upset, American teenager CiCi Bellis downed eighth-seeded Svetlana Kuznetsova 6-4, 7-5. Bellis won 74 percent (39-of-53) of her first-service points and broke the 32-year-old Russian three times.
The 18-year-old Bellis, ranked 36th in the world, broke Kuznetsova in the first game of the first set and twice more in the second, including in a crucial 11th game that gave her a 6-5 lead.
"I think I played really well today," Bellis said following her second career win against a top-10 opponent. "Obviously I told myself I had to because she's unbelievable."