The couple has a three-year-old son, Zidaan, and the new entrant in the family will be called Aariz.
Zayed's close friend, designer Manav Gangwani, confirmed the news on twitter.
"Came to Mumbai to celebrate the birth of my Best Friend - my Brother Zayed's & Malaika's 2nd Baby!," Gangwani wrote on twitter.
Dia Mirza, who has opened her production house in partnership with Zayed, tweeted,
"Someday's you experience the entire cycle of life. Malaika and Zayed were blessed with the birth of their second child! A beautiful boy (sic)."
Zayed is looking forward to the release of his maiden home production, 'Love Breakups Zindagi'. The film, produced under their banner Born Free Entertainment, will release on October 7.