The driver took the woman to a parking lot in nearby Markham where she was allegedly sexually assaulted, police said.
Ahmadfayim Bayat, 30, is now charged with one count of sexual assault, police said.
They say Uber has been co-operative in the investigation.
Bayat is due in court later Wednesday for a bail hearing.
Susie Heath, a spokeswoman for Uber, said in an email that the company takes “every safety incident very seriously and are committed to the safety of everyone who uses Uber.”
“Upon hearing of this disturbing incident, we immediately removed the driver from the platform and contacted York Regional Police to offer our assistance and have supported them in their investigation,” Heath added.