During the meeting, Zardari appreciated Malik's cricketing skills and said sportspersons were ambassadors for their country.
"Sportspersons earn a name for their country through their excellence in sports and contribute to the real potential and image of their country," he said.
Malik and Mirza are currently on a private visit to Pakistan. The cricketer hopes his marriage with Mirza will help in improving relations between Pakistan and India.
Malik further said he hoped that bilateral cricket ties with India would resume soon. Mirza, who recently suffered a knee injury, is on holiday while Malik is playing in Pakistan's National Twenty20 Championship.
Over the past few days, the couple visited Malik's hometown of Sialkot and travelled to Lahore on a private visit.
Mirza will be in Karachi for the duration of the National Twenty20 Championship, in which Malik is captaining the Sialkot Stallions.
"I am here to play cricket and my wife is with me on a holiday, but obviously her presence is good for me and I hope to do well in the national tournament," he said.