The London Olympic bronze-medallist lost on points to United States' Virginia Fuchs in the Brazilian city, which will host the Olympic Games next year.
This was Mary Kom's first competitive appearance in over a year. She had been laid low by a shoulder injury after winning the gold medal at the Asian Games in Incheon last year.
Four other Indians, in the men's draw, also bowed out of the ongoing competition after losing in the semifinals, bringing an end to India's campaign.
In other fights, Parveen Kumar (91kg) was beaten by local favourite Gidelson De Oliveira. Shyam Kakara (51kg), on the other hand, went down to Hasanboy Dusmatov of Uzbekistan.