The incident occurred about 3 a.m. Saturday at the Uniun, the Toronto Star reported.
"The fan was just a small little guy," said Orin Bristol, the nightclub's operations manager. "He wasn't being aggressive.
"Security was a bit aggressive. There weren't punches thrown really; it was more of a shoving match and pushing match."
The nightclub employee said there were no injuries and that Bieber somehow lost a $40,000 gold chain during the incident.
The Star said Toronto police had not been informed of the confrontation as of Saturday night.