The Danish teenager, who triumphed in Ponte Vedra, Florida last week, reached the semi-finals with a 6-3 6-4 win over sixth-seeded Russian Nadia Petrova after former world number one Jankovic lost 1-6 6-3 6-3 to Slovak Daniela Hantuchova.
Hantuchova, who had not beaten the second-seeded Serb since 2006, broke serve six times in a match that took two hours and 18 minutes on the green clay of the stadium court.
Wozniacki, who lost in last year's final to German Sabine Lisicki, enjoyed her second win over Petrova in a month after toppling the Russian in the fourth round at Indian Wells.
Eighth seed Hantuchova will play Australia's fourth-seeded Samantha Stosur, who took just an hour to put away China's Peng Shuai 6-4 6-1. Wozniacki next faces American Melanie Oudin or Russia's Vera Zvonareva, who play later on Friday.
(Writing by Frank Pingue in Toronto; editing by Ken Ferris)