TfL concluded the ride-hailing app firm was not fit and proper to hold a London private hire operator licence.
It said it took the decision on the grounds of "public safety and security implications".
Confirming it would appeal against the decision, Uber said it showed the world "far from being open, London is closed to innovative companies".
Some 3.5 million passengers and 40,000 drivers use the Uber app in London.
Latest updates and reaction
In a statement, Uber said: "Transport for London and the mayor have caved in to a small number of people who want to restrict consumer choice."
Uber's general manager in London Tom Elvidge said: "To defend the livelihoods of all those drivers, and the consumer choice of millions of Londoners who use our app, we intend to immediately challenge this in the courts."
He said Uber operated in more than 600 cities around the world, including more than 40 towns and cities in the UK.
There had been growing speculation that the app could be banned from London.
Opponents of the firm claim it causes gridlocked roads and does not do enough to regulate its drivers.
TfL's concerns include Uber's approach to carrying out background checks on drivers and reporting serious criminal offences.
Analysis: From BBC transport correspondent Rory Cellan-Jones
Throughout its short, tempestuous life, Uber has clashed with regulators around the world - and more often than not it has come out on top.
Its tactic has often been to arrive in a city, break a few rules, and then apologise when it's rapped over the knuckles. Some regulators have backed down, others have run the company out of town.
In London, despite protests from angry taxi drivers, the company has had a relatively easy ride until now. But a wave of bad publicity about its corporate culture, its lax attitude to checks on its drivers and its treatment of this freelance army seems to have spurred TfL into action.
Make no mistake, Uber will use every legal avenue to fight this ban. It will argue that consumers, in the shape of the millions of mainly young Londoners who rely on its service, will be seriously let down if it can no longer operate. But the courts will have to balance that with the serious concerns about public safety raised by TfL.
Mayor of London Sadiq Khan said in a statement: "I fully support TfL's decision - it would be wrong if TfL continued to license Uber if there is any way that this could pose a threat to Londoners' safety and security.
"Any operator of private hire services in London needs to play by the rules."
General secretary of the Licensed Taxi Drivers' Association Steve McNamara said: "The mayor has made the right call not to re-license Uber.
'Luddite decision'
"We expect Uber will again embark on a spurious legal challenge against the mayor and TfL, and we will urge the court to uphold this decision.
"This immoral company has no place on London's streets."
Across the world, Uber has been pushed out or denied access by local licensing laws.
Legislators in Darwin, in Australia's Northern Territory, are debating whether to allow Uber to return after a raft of reforms designed to open up the ride-sharing market were announced.
Uber is currently fighting a test case in Denmark after four if its drivers were found to be in violation of the country's laws requiring taxi meters.
Timeline: Uber
July 2010 - Uber is launched as a cab-hailing app in San Francisco
July 2012 - Uber is granted a five-year private hire licence to operate in the capital
May 2017 - Uber is issued a four-month operator licence to continue working in London to allow TfL to "consider" a new five-year deal
18 September 2017 - TfL announces it is overhauling the current fee structure for private hire companies operating in the capital
22 September 2017 - TfL announces it will not be issuing Uber London Limited with a private hire operator licence
David Leam, director of infrastructure at London First, a London business lobbying group, said: "This will be seen as a Luddite decision by millions of Londoners and international visitors who use Uber.
"It will also hit London's reputation as a global tech hub. London needs to be open to new ideas, businesses and services."
Uber has 21 days to appeal.
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