The top-ranked Williams returned to play last week in Stanford, California, and won her tour-best fourth title of the season. The event was her first since she withdrew from a doubles match at Wimbledon because of equilibrium problems.
"I served great," said Williams, celebrating her 200th week at No. 1 in the world. "I needed to serve great because she was hitting unbelievable serves to me."
Williams has won the Rogers Cup three times when it is held on alternate years in Toronto, including last year, but she had not played in Montreal since she retired from the final with an injury in 2000.
"I felt really comfortable and confident," Wozniacki said. "I served and returned well. She's a tough player. She has some big shots. I was just able to neutralize them and play my game."
The 11th-seeded Wozniacki, coming off a victory in Istanbul, has dropped only six games in three matches this week.
"It will be a great match," said Williams, 6-1 against Wozniacki. "She's playing great tennis. She's really focused. It will be a good match to see where I am."
In other matches, Spain's Carla Suarez Navarro upset fourth-seeded Maria Sharapova 6-2, 4-6, 6-2 in a match delayed twice by rain, and Russia's Ekaterina Makarova topped second-seeded Wimbledon champion Petra Kvitova 6-4, 1-6, 6-2.
"I couldn't find my rhythm from the beginning of the match," Sharapova said. "I always had my back against the wall, always had to come back."
Third-seeded Agnieszka Radwanska will face eighth-seeded Victoria Azarenka in the other quarterfinal. Radwanska beat Sabine Lisicki 6-1, 3-6, 6-3 in the late match, and Azarenka topped Heather Watson 6-2, 6-4.