One man, named as Ahmed Abdallah, was killed in the incident.
Forty-six others were injured, including 12 with bird shots and two with live ammunition.
Alexandria security chief, Amin Ezz Eddin, said Wednesday that security forces had managed to control the encounters which erupted after evening prayers at Qaed Ibrahim Mosque, a regular focal point for protests over the past two years.
Ezz Eddin told state-run news agency MENA in an exclusive statement that violence took place when Brotherhood supporters chanting slogans against the army angered residents .
Scuffles between both sides developed into an exchange of fire before the police intervened.