Hussain emerged as a clear winner in the one-sided contest with ex-judge Wajihuddin Ahmad of Pakistan Tehreek-i-Insaf party, state media reported.
Pakistan People's Party withdrew its candidate Raza Rabbani and boycotted the election in protest to the date of polls being changed.
The polling started at 10.00 AM amidst tight security arrangements.
Born in the historic city of Agra, Hussain, who belongs to an Urdu-speaking ethnic group that migrated from India during partition in 1947, was the candidate of ruling PML-N government.
The office of the president is ceremonial in Pakistan but he is still the constitutional chief of the armed forces but cannot order deployments.
He also appoints the services chiefs at the recommendation of the prime minister.
Pakistan so far had 11 presidents, out of which five were military generals. Four of them seized powers through coups, whereas first president Major Sikandar Mirza was elected in 1956 after the first constitution was adopted.
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