Police said about 100 people attended the protest outside the New Scotland Yard building, many carrying banners urging "justice for Muslims" and calling on the police to stop "terrorising our community".
Massoud Shadjareh, from the Islamic Human Rights Commission and a protest organiser, said the raid sent a message to Muslims that they were not equal citizens.
"We are shooting innocent people, knowing that we are doing it, and then saying it is acceptable," he said.
The two men, brothers Abul Koyair, 20, and Mohammed Abdul Kahar, 23, were detained on June 2 after up to 250 police officers, some in chemical suits, raided a house in the east London suburb of Forest Gate.
Kahar was shot in the shoulder during the incident. Both men were released without charge on Saturday after police found no evidence of an alleged chemical bomb.
'Series of mistakes'
Both men are considering legal action against the Metropolitan police, British newspapers said on Sunday.
The police, who have come under heavy criticism for the raid, have apologised for the disruption caused by the raid but said they had no choice but to act on "very specific intelligence".
"We hope that the appropriate lessons will be learned by all involved in this tragic incident"
Muhammad Abdul Bari, secretary general of Muslim Council of Britain
However, the Metropolitan Police Authority, which monitors the police, said a "series of mistakes" had been made.
Muhammad Abdul Bari, secretary general of the influential Muslim Council of Britain, also said lessons should be learned from the raid and warned that it could radicalise young, disenchanted Muslims in the UK.
"This decision to release the two brothers without charge confirms their innocence, and we hope that the appropriate lessons will be learned by all involved in this tragic incident," he said.