Fernandez, who defeated three top-5 players before going down to fellow teenager Emma Raducanu in the 2021 US Open final, came back from a double match point down in the second set before prevailing over Rybakina.
Rybakina was playing her first match since falling in the Wimbledon semifinals to eventual champion Barbora Krejcikova. Acute bronchitis had forced the Kazakhstani to withdraw from both the Paris Olympic Games and last week's WTA 1000 event in Toronto, and her rust showed throughout in the form of 17 double faults.
Two of those came on both of her match points as she served at 6-5 in the second set.
Fernandez has been enjoying a resurgent season and returned to the Top 30 in June after an absence of nearly two years.
The Canadian, currently ranked 23rd in the WTA Rankings, took advantage to seal her fifth career Top 5 win, and first since she knocked out three Top 5 opponents to reach the 2021 US Open final.
Earlier on Wednesday night, World No.1 Iga Swiatek made a winning return to the hard courts at the Cincinnati Open. Playing her first match since winning a bronze medal for Poland at the Paris 2024 Olympics, Swiatek held off Varvara Gracheva 6-0, 6-7(8), 6-2 in her tournament opener.
A semifinalist last year, Swiatek will face Marta Kostyuk next in the third round. Kostyuk advanced by defeating Lulu Sun 6-3, 7-5.
