Zardari, who assumed charge as president on Tuesday, visited the Bhutto family mausoleum in Garhi Khuda Baksh village in Sindh province amid tight security.
Zardari offered prayers and laid a floral wreath on the the grave of Bhutto, who was killed in a gun-and-suicide attack on December 27 last year.
He also paid respect at the grave of Bhutto's father Zulfikar Ali Bhutto during the private visit, the state-run APP new agency reported.
Zardari, 53, was made the co-Chairman of the Pakistan Peoples Party along with his son Bilawal Bhutto Zardari after his wife's assassination. The PPP and its allies formed the government in March after emerging victorious in the February 18 general election.