Marco Archer Cardoso Moreira, 53, was arrested in 2003 after police at Jakarta airport found 13.4 kg of cocaine hidden in his hang glider.
Brazil says he was the first Brazilian national to be executed abroad and has warned it will damage relations. Five other convicts from Indonesia, Malawi, Nigeria, Vietnam and the Netherlands, were executed on Sunday.
Convicted of drugs charges, they faced a firing squad in Central Java province shortly after midnight local time.
Five were executed on the island of Nusa Kambangan and the other one, a Vietnamese woman, was executed in the small central Javanese town of Boyolali.