Sufia is the daughter of Chennai-based businessman Syed Nizamuddin.
The wedding was a closely-guarded affair and was attended by select invitees.
Mammootty, who'd paid a visit to Tamil Nadu Chief Minister J Jayalalitha on December 20 to invite her for the wedding, had reportedly taken a break from work to prepare for his son's big day.
He will be hosting a reception for the newly-married couple in his hometown Kochi on December 26.