A Muslim rights group official said at least five people may have been killed.
Faisal was visiting the east African nation on a preaching tour. Kenyan intelligence officials said they fear his speeches could stoke radicalism in a country that has suffered two al-Qaeda-linked attacks.
|Police fired tear gas to quell the protests forcing people back to the mosque [AFP]
Some Kenyans, angry the attempted protest had taken place at all, joined the security forces and began hurling stones at the marchers, squeezing them back towards the mosque.
"This is not an acceptable behaviour. The man who is supposed to be deported is not a Kenyan and his presence is not in the interest of Kenya these days," one witness said.
Many protesters, some carrying pictures of Faisal on placards, were eventually forced back into the mosque.
Faisal was deported from the UK in 2007 for preaching racial hatred and urging his listeners to kill Jews, Hindus and Westerners. He was arrested in Kenya on December 31.
Otieno Kajwang, Kenya's immigration minister, has declared Faisal a prohibited immigrant.
Attempts by Kenya to deport him failed last week after Nigeria refused to give him a transit visa to Gambia.
A police source said the government was holding him in custody until he could be deported straight to Jamaica.
"One person, a Jamaican ... How can he make the whole country shut down? One person, how come no one in Jamaica is defending him?" a witness at the protests said.
"These demonstrators, they can go back home to Somalia if they want to," he told the Reuters news agency.
Kenya hosts about 300,000 Somali refugees in refugee camps and there is a significant Somali community in Nairobi.
There have been reports of supporters of Somalia's al Shabab rebel group recruiting fighters and young suicide bombers from the diaspora within Kenya.
Al Shabab, accused of having links to al-Qaeda, is battling to overthrow the Somali government and impose their own version of sharia law.