Police said evidence has linked the suspect to the alleged crimes that took place eight months apart, one in 1993 and the other in 1994.
In one incident, police said a 19-year-old woman was pulled under a parked tractor-trailer where she was sexually assaulted and then robbed by a man armed with a knife.
In the other, police said a man climbed up to a second-storey apartment and sexually assaulted a 46-year-old woman at knifepoint before stealing her purse.
The arrest came more than a year after police offered a $50,000-reward for information that led to the identification or capture of the suspect.
Toronto police Det. Ali Ansari said 43-year-old Steven John McGuire was arrested last week in Fort McMurray, Alta., where he had been working.
He is charged with sexual assault with a weapon and robbery in the 1993 incident, and breaking and entering, sexual assault with a weapon, robbery and threatening death in the 1994 incident.
McGuire appeared in court Sunday and was remanded into custody. His next hearing is scheduled for Jan. 21.
Police revealed few details Monday about the investigation, saying they couldn't discuss the nature of the tip they received.
But Ansari said McGuire has been living outside Ontario since 2005 and is known to police in several jurisdictions, including Toronto.
"We want the community to know that we don't give up on cases," he said in a news conference, adding the victims were "relieved" to hear of the arrest.
Police have released a composite sketch of McGuire in the hopes of stirring up more information.