The police took control of the city centre that was held by protesters for five months. With helicopters hovering overhead, officers entered Oaxaca from several sides on Sunday, setting off fierce street battles.
They marched up to a final metal barrier blocking the city centre, but pulled back as protesters armed with sticks attacked them from behind, hurling burning tyres. The air filled with black smoke and tear gas.
A 15-year-old boy manning one barricade was killed by a tear-gas canister, human-rights worker Jesica Sanchez said.
As night fell, however, protesters abandoned the centre and regrouped at a university.
They pledged to continue their battle to get Ulises Ruiz, the regional governor, to resign, even as police tore down the banners and tents that had served as their headquarters for months of often violent demonstrations.
Protest spokesman Roberto Garcia said 50 supporters had been arrested and police were searching houses, looking for protest leaders. Police did not immediately confirm that.
Vicente Fox, the Mexican president, who leaves office on December 1, had resisted calls to send federal forces to Oaxaca until Saturday, a day after gunfire killed a US activist-journalist and two residents.
Police inspecting a burnt bus in
Oaxaca after Sunday's clashes
The protests began in May as a teacher's strike in this colonial southern Mexican city of roughly 275,000.
But the demonstrations spiralled as anarchists, students and Indian groups seized the central plaza and barricaded streets throughout the city to demand Ruiz's removal.
Police and state forces - often in plainclothes - have shot at protesters, setting off clashes in which at least eight people have died.
Protesters accused Ruiz of rigging his 2004 election and using thugs to kill or crush political opponents.
They say his resignation is not negotiable and they will not return home without it. The violence has driven tourists from one of Mexico's most popular destinations, forcing hotels and restaurants to close their doors.
Late on Saturday, protesters gathered to mourn Bradley Roland Will, 36, of New York, who was killed during a shootout between protesters and men they claim were local officials in Santa Lucia del Camino on Oaxaca's rough outskirts.
Will, whose body was laid out in a white shirt and a glass-topped coffin at a funeral parlour near the square, was remembered as a video and documentary-maker devoted to the protesters' cause.
A video posted by Indymedia.org showed the last minutes of footage Will shot on Friday, apparently including the moment he was hit by gunfire.
Protesters accuse the governor
of rigging the 2004 election
In a statement, Will's family said it was "grieving over the tragic and senseless loss of Brad's life".
US Ambassador Tony Garza said in a statement that those who shot Will may have been Oaxaca police, and Mayor Manuel Martinez Feria of Santa Lucia del Camino said five men seen brandishing pistols at the time of the shooting had been turned over to authorities.
Garza identified them as two members of Santa Lucia's city council, two of that town's police officers and a former justice of the peace from another town.
In Mexico City, several hundred supporters of the Oaxaca protests converged on a hotel where Ruiz was rumoured to be staying, damaging the grounds and screaming "Murderer! Murderer!"
The protesters estimated that around 4,000 federal police had taken up positions around the edges of Oaxaca. There were no official reports, however, on how many officers were deployed.