"President Dilma Rousseff has accepted minister (Antonio) Patriota's resignation," a government spokesman told AFP, adding that he would be succeeded by Luis Alberto Figueiredo, Brazil's UN ambassador.
A Brazilian diplomat had revealed earlier yesterday that he helped a Bolivian opposition senator escape to Brazil after he was holed up for 15 months in Brasilia's embassy in La Paz despite having been granted asylum.
Senator Roger Pinto, an opponent of Bolivian President Evo Morales, made his escape Friday in an embassy car escorted by Brazilian marines, driving 22 hours to the southwestern Brazilian city of Corumba, 1,600 kilometres (1,000 miles) from La Paz.
The diplomat said he made the personal decision to help Pinto escape "because there was an imminent threat to the life and dignity of the senator."
He said Pinto was suffering from depression and was contemplating suicide.
The Bolivian government views Pinto as a fugitive from justice after he was accused of corruption, for which he was sentenced to a year in prison.
His case strained relations between La Paz and Brasilia. Morales last year said Brazil's decision to grant Pinto asylum was "a mistake."
In La Paz, Bolivian Foreign Minister David Choquehuanca expressed "deep concern over the transgression of the principle of reciprocity and international courtesy."
"Under no condition could Senator Pinto leave the country without a safe conduct pass," Choquehuanca said.