Around 250 people had taken to the streets on Monday, dousing the capital's security minister in pink glitter and smashing the glass doors of the local prosecutor's office.
The protests were in response to two recent cases: that of a 17-year-old girl who says four policemen raped her in their patrol car as she left a party on the capital's north side, and that of a 16-year-old girl who says a policeman raped her at the national photography archive museum, in the city center.
"Six police have been suspended from their duties while the investigation continues," said Mayor Claudia Sheinbaum, the first woman elected to the job, in a video posted to Twitter. "There will be no impunity nor any fabrication of guilt.
The rapes are the latest incidents to trigger outrage over the high rate of violence against women and girls in Mexico.
One policeman was already arrested Thursday in the case that occurred at the museum.
In addition to covering the capital's security minister, Jesus Orta, with glitter as he appealed for calm, the protesters, who were mostly women, spray-painted a group of policemen and displayed a pig's head outside the local prosecutor's office.
Masked demonstrators later hurled rocks at the building, shattering the glass entrance.
Machismo plays a prominent role in Mexican culture, and levels of violence against women and girls are high in the country.
Nine women are murdered in Mexico every day, according to the United Nations.