Mr Xi, appointed to the Communist Party's top post in November, replaces Hu Jintao, who is stepping down.
Some 3,000 deputies to the National People's Congress, the annual parliament session, took part in the vote at the Great Hall of the People.
The new premier - widely expected to be Li Keqiang - is scheduled to be named on Friday, replacing Wen Jiabao.
While votes are held for the posts, they are largely ceremonial and the results very rarely a surprise.
Mr Xi, who bowed to the delegates after his name was announced but made no formal remarks, was elected by 2,952 votes to one, with three abstentions.
He was named general secretary of the Communist Party on 8 November and also given the leadership of the top military body, the Central Military Commission.
China's parliament engaged in a political ceremony that involved all the hallmarks of a real election: a ballot box, long lines of delegates queuing to vote, and a televised announcement of a winner. However, no-one was surprised to hear the results: with a whopping 99.86% of the vote, Xi Jinping was anointed President of the People's Republic of China and Chairman of the People's Liberation Army.
In November, Mr Xi was elevated to the top spot in China's Communist Party. However, he did not become the country's official head of state until his candidacy was approved by China's parliament.
According to China's constitution, almost 3,000 NPC delegates are allowed to "elect" candidates for the state's top positions. However, in practice, delegates merely endorse the names put forward by the party.
Perhaps the only interesting result of the election is that Mr Xi did not receive 100% of the ballot. One person voted against him and three people abstained. The result leaves some in China to wonder: perhaps, in an act of modesty, Mr Xi voted against himself.
This vote, handing him the role of head of state, was the final stage in the transition of power to him and his team, the slimmed-down, seven-member Standing Committee.
The largely symbolic role of vice-president went to Li Yuanchao, seen as a close ally of Mr Hu and a possible reformist.
The 61-year-old, who is not a member of the Standing Committee, has in the past called for reforms to the way the Communist Party promotes officials and consults the public on policies.Austerity president
The son of a revolutionary veteran, 59-year-old Mr Xi held top party roles in Zhejiang and Shanghai, before being appointed to the Standing Committee - China's top decision-making body - in 2007.
Since his elevation to the top of the party in November, Mr Xi has been feted in Chinese media as a man of the people who shuns the usual trappings of his position.
He has spearheaded an austerity drive for officialdom, in a move seen as an attempt to address rising public anger over the perceived luxurious lifestyles of leaders.
He has also been widely quoted in state media on the need to stamp out corruption at all levels, warning of civil unrest if party privilege is not tackled.
Considered a "princeling" given his family connections - his father was one of the Communist Party's founders
Sent at the age of 15 to work in a remote village for seven years when his father was purged from power before the Cultural Revolution
Reportedly tried to join the Communist Party at least nine times but was rejected because of his father's issues
Married to Peng Liyuan, a famous Chinese singer who is also a major-general in the Chinese army
The party faced many challenges, he said in a speech after assuming the Communist Party leadership.
Problems such as "corruption and bribe-taking by some party members and cadres, being out of touch with the people, placing undue emphasis on formality and bureaucracy" had to be addressed, he said.
Mr Xi assumes the leadership of a nation that is growing wealthier but more vocal in its anger at issues such as rising inequality, environmental damage and food safety.
He also faces concern among regional neighbours over how China will wield its rising power, particularly in relations to thorny issues such as territorial disputes with Japan and Asean nations.
Xi Jinping is expected to make his first overseas visit as president to the BRICS summit in South Africa at the end of March.
He is also expected to visit Russia, the foreign minister said.
On Friday Premier Wen Jiabao's successor will be named, with the party's number two leader, former Liaoning party chief Li Keqiang, set to take over.
