Investigators said that after being stalled for more than two decades, the break in the case came by using forensic DNA evidence collected at the time of the incident.
Shane Daniel Garry, 45, of Brampton, Ont., was arrested Thursday and charged with two counts of kidnapping, two counts of forcible confinement, sexual assault, sexual interference, threatening bodily harm and two counts of abandoning a child under the age of 10.
Police said Garry appeared in court Friday. The allegations against him have not been proven.
Det. Ali Ansari said Garry was "known to police" but would not provide any details.
The detective, who works exclusively on cold cases, said advances in DNA testing allowed investigators to make headway on the case.
"In 1991, the DNA technology was not where it is now," Ansari said. "In fact, it was non-existent almost."
The nine-year-old girl and her five-year-old sister were playing in the lobby of their east-end apartment building on Feb. 3, 1991, when police say a man approached them and asked for help finding a place to eat.
It's alleged the man asked the girls to get in his car, then dropped the five-year-old off at a store before taking the nine-year-old to a secluded area, sexually assaulting her and then leaving her at a restaurant.
Ansari said the two sisters, now in their late 20s and early 30s, are relieved there is an arrest in the case after so many years.
"They were surprised and happy," Ansari said, adding they have found a way to get on with their lives after what happened to them.
"Both of them are 22 years older... they’re working, they have dealt with it somehow. I don't know the extent of it, I don’t think anybody could say with certainty how they have dealt with the incident that occurred to them when they were children."
Photos of Garry from December 1990 and January 1993, as well as a current photo have been released by investigators, who said they believe there may be other victims.
Anyone with information is asked to contact Toronto police or Crime Stoppers.