Menezes' mother, Maria, almost collapsed in tears and was held up by her husband and relatives after she laid a single rose on her son's casket.
People in the crowd released dozens of green and yellow balloons into the air, the primary colours of the Brazilian flag.
Then they applauded - a common Brazilian tradition at burials of people considered well-known or important - just before the casket was lowered into the ground.
Police estimated more than 10,000 people passed by the casket earlier as it lay draped with the Brazilian flag at the Sao Sebastiao Church in Gonzaga, a town of 6,000 where many head abroad to make money so they can return for a better life back home.
In London, friends and relatives lay flowers at the subway station where Menezes, an electrician, was shot exactly a week earlier as he entered a subway on his way to fix an alarm.
"Even if it is true that his visa had expired, that does not justify what the police did to him"
Giovani de Menezes,
relative of the deceased
Bianca Jagger addressed a requiem mass in Westminster Abbey held for Menezes led by Father Frederico Ribeiro, the chaplain of the local Brazilian community.
In Gonzaga, homes and small businesses were festooned with streamers and balloons painted green, white and yellow.
Though no protests were planned, signs on buildings showed that residents are still outraged.
Calls for justice
His relatives dispute accounts that Menezes was wearing a bulky jacket and ran from police. "We Want Justice," said one sign. Another read: "Jean, Martyr of British Terrorism."
Friday was declared a municipal holiday because "the entire town has been traumatised," Zacharias said. "It is as if everyone is carrying an enormous weight of sadness on their shoulders."
In a statement, Brazil's Foreign Ministry said the status of Menezes' visa "in no way alters the responsibility of British authorities for the tragic death of an innocent, peace-loving Brazilian citizen".
Relatives and friends are
demanding justice for the killing
"It must bear no influence on the investigation of the tragedy or on the measures the British government should adopt in terms of compensation to Jean-Charles de Menezes' family," the statement said.
Menezes' brother Giovani de Menezes told the Folha de Sao Paulo newspaper that his brother had said he had a multiple entry two-year visa allowing him to work legally in Britain.
"Even if it is true that his visa had expired, that does not justify what the police did to him," Giovani de Menezes said.