Mr Xi was elected by 2,952 votes to one, with three abstentions.
The ritual ballot took place at Beijing's Great Hall of the People.
"Now I announce comrade Xi Jinping is selected as president of the People's Republic of China," said Liu Yunshan, who was chairing the National People's Congress (NPC).
Mr Xi, 59, 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.
A new premier is scheduled to be named on Friday, replacing Wen Jiabao.
Li Yuanchao, an ally of Mr Xi, was elected to be vice-president.
It was China's second orderly succession since Communist party rule began in 1949.
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