The result pushed the European side up into fourth place, level on points with their South American rivals, but with a better points difference and head-to-head record.
The defeat means Brazil finish the eighth-finals stage in fifth place and exit the tournament before the knockout phase has got under way.
Czech Republic started the clash the brighter of the two sides and immediately raced into a 24-18 lead at the end of the first quarter.
And they managed to maintain their advantage following an eventful second period to go into the interval 40-34 in front.
Yet a devastating third quarter from the European side saw them claim 24 points compared to Brazil’s 12 and put the game beyond reach of their opponents.
A strong final 10 minutes from Brazil was not enough to prevent defeat as their Group F rivals, helped by a 23-point haul from Katerina Elhotova, emerged victorious by a 12-point winning margin.
Penthathlon Tokyo 2020 Line-up
Aberdeen Standard Investments Ladies Scottish Open