Hussain, 73, will be sworn in on September 9 at the presidential palace due to be vacated by incumbent Asif Ali Zardari, who is stepping down at the end of his five-year term.
Hussain emerged as a clear winner in the contest with ex-judge Wajihuddin Ahmed of Pakistan Tehreek-i-Insaf party, state media reported.
Pakistan People’s Party had withdrawn its candidate Raza Rabbani and boycotted the election protesting change of poll dates from August 6 to July 30 on Supreme Court's directions.
Lawmakers from both houses of the national parliament and four provincial assemblies voted in the two-man race for the top post.
Announcing the results, Chief Election Commissioner Fakhruddin Ibrahim said, "Mr Mamnoon Hussian got 432 vote of the electoral college and has been declared as elected".
Ahmed got 77 of the total 887 polled votes. At least nine ballots were declared invalid as they were wrongly marked by the voters, he said.
More than 1,100 National and provincial lawmakers were eligible to participate in the polls but some of them were absent while those associated with PPP stayed away due to their boycott.
The polling started at 10.00 AM amidst tight security arrangements and was over by 15:00 PM.
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.
Hussain, who will be president for five years, resigned his membership of the PML-N soon after the election results were announced.
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 has 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.
Former Sindh governor and an alumnus of the Institute of Business Administration, from where he graduated in 1965, Hussain is an old loyalist of Nawaz Sharif and remained with the PML-N during the regime of former military ruler Pervez Musharraf.
He served as the governor of Sindh from June to October 1999 and lost the post after the then army chief Gen Pervez Musharraf toppled the PML-N government in a military coup in Oct 1999.
"Describing the office of president as the symbol of federation, the presidential candidate pledged to serve the country and its people in his capacity as president," a statement issued by Sharif's office said.