The 27-year-old took 90 minutes to secure victory against the Brazilian, who she beat on her way to winning the San Diego Open earlier this month.
Boulter reached the last 16 of the tournament for the first time and will now face Victoria Azarenka of Belarus.
World number two Aryna Sabalenka went down 6-4 1-6 6-1 to Anhelina Kalinina.
In what was her second match following the death of her former boyfriend and ex-NHL player, Konstantin Koltsov, Sabalenka's emotions spilled over.
The Belarusian reacted angrily to the defeat, smashing her racket into the floor of the court.
Murray beats Etcheverry to reach third round of Miami Open
Koltsov died at the age of 42 on Monday in what police described as an "apparent suicide" in Miami.
"It's always tough to play on big stages against these top players," said Kalinina, who will play Kazakhstani Yulia Putintseva in the next round.
"Today was really tough with nerves but I managed in the tough moments to deal with it."
Polish world number one Iga Swiatek breezed past Italy's Camila Giorgi 6-2 6-1 in 67 minutes.
Japan's Naomi Osaka, who returned to the tour at the end of last year after giving birth, continued her resurgence with a 6-2 7-6 (7-5) win over Elina Svitolina of Ukraine.
Sixth seed Ons Jabeur of Tunisia suffered a shock 6-1 4-6 6-3 defeat by world number 65 Elina Avanesyan of Russia.
Avanesyan's compatriot Anna Kalinskaya also progressed with a 6-3 6-1 victory over Latvian ninth seed Jelena Ostapenko.