"Yes he has cast his vote through a postal ballot," presidency spokesman Farhatullah Babar told AFP.
The Taliban have directly threatened Zardari's Pakistan People's Party (PPP) and its main secular coalition partners, which the party says dramatically curtailed its ability to campaign in public.
Zardari's wife, former prime minister Benazir Bhutto, was assassinated in a gun and suicide attack in 2007 before the last election and her successor as PPP chairman, their son Bilawal Bhutto Zardari, is too young to run.
It is unclear whether Bilawal will even vote. Party officials have said the threats against him are too serious for him to appear in public.
Babar confirmed to AFP that Bilawal had been denied permission for a postal ballot but did not give an explanation.
Zardari's two daughters, Aseefa and Bakhtawar, also cast their votes by post, the spokesman said, providing no further information. The precise whereabouts of the family has not been announced.