By Agence France-Presse
Thousands of doctors, teachers and students had taken to the streets to demand the government abandon plans to privatize the health and education sectors.
Firefighters came to extinguish the blaze, which destroyed the diplomatic mission's gate without damaging the main embassy building.
The US embassy issued a statement after the attack urging Hondurans to refrain from "acts of violence."
Police spokesman Jair Meza told local media that one of the suspects, a 23-year-old man, had been arrested.
Relatives of the suspect later went with a crowd to the police headquarters where they shouted demands for his freedom.
Demonstrators blamed "government infiltrators" for the damage to the embassy.