Napolitano, 87, received 738 votes from Parliament Saturday, while the only other candidate, Stefano Rodota, who was backed by the M5S Party, received 217 votes, Italy's ANSA news agency reported.
The president previously said he would not seek a second term.
"I am convinced that the founding fathers conceived the role of President of the Republic as measured in seven year terms," Napolitano said in March.
"It is not a coincidence that no other president has served a second term. There are age factors and its limitations to consider."
However, Democratic Party leaders failed to agree on his successor and asked him to remain at his post, Britain's The Guardian newspaper reported.
Beppe Grillo, head of M5S, denounced Napolitano's re-election as a "coup d'etat" that would "prevent change" and called for a protest in Rome.