The match, which gave Luiz Felipe Scolari the first win of his second stint as Brazil coach, was held in aid of the family of a young fan killed by a flare last month.
Neymar scored in the 30th and 41st minutes after fellow striker Leandro Damiao had put Brazil ahead after three minutes.
Midfielder Leandro, who replaced Ronaldinho in the 77th minute, scored the fourth in a counter-attack one minute into added time.
Striker Alexandre Pato, who returned home this year to join Corinthians from AC Milan, came on in the second half replacing Leandro Damiao in his first appearance for the 2014 World Cup hosts since August.
Teenage fan Kevin Beltran Espada was killed by a flare allegedly launched by Corinthians fans in the Bolivian city of Oruro where the Brazilian team began the defence of their South American Libertadores Cup title against San Jose in February.
Bolivia, one from bottom of the South American World Cup qualifying group with little chance of making it to the finals, are preparing for qualifiers in June against Venezuela and Chile.