The conflict began months ago as a teachers' strike against poor pay turned into a broad protest against social and economic conditions in the poor Mexican state.
Between May and October, thousands of protesters seized and paralyzed much of the city before being dislodged by police.
Florentino Lopez, the protester's spokesman, told local media that the demonstrators would set up their protest camp again in the Santo Domingo plaza on Monday.
Federal police broke up the camp by using tear gas and water jets from tankers.
The previous day masked youths broke away from a protest march and hurled petrol bombs, fireworks and rocks at federal police in a failed attempt to re-take the city's main plaza.
On Sunday, the police removed protesters from the nearby Santo Domingo plaza, where they had regrouped after police re-entered the city in late October, ending a five-month takeover.
Police patrols stepped up
The federal police, who have largely remained in the main square and a few positions around the city, said they would actively patrol the city in search of those who committed "direct attacks" against them.
The police said that four of their officers and several bystanders had been injured in the confrontation.
They accused outside activists of playing a key role in the weekend's
The latest troubles left three hotels damaged, more than 20 cars burned out and parts of Oaxaca's lawcourts gutted by fires.
Protesters also tossed petrol bombs at a tax office.