Hundreds of people queued outside Paddington station in west London to be on the first train when it left at 6.33am.
London Mayor Sadiq Khan called the opening "historic" and "the most significant addition to our transport network in decades".
"The Elizabeth line is much more than just a new railway – it will provide a crucial economic boost to the whole country and help to turbo-charge our recovery from the pandemic," he added.
Khan's predecessor as mayor, Prime Minister Boris Johnson, said the project is forecast to boost the UK economy by £42 billion.
Only one of the line's three branches has opened, from Paddington to Abbey Wood in southeast London.
Sections from Shenfield, east of London to Liverpool Street and Heathrow Airport and Reading, west of the capital, to Paddington will open by May next year.
The line, named after Queen Elizabeth II, is projected to carry up to 200 million passengers a year, adding 10 percent more capacity to London's transport network.
Work started on the project back in 2009 and was initially called Crossrail. It was originally due to open in 2018.
But it was hit by problems with construction and complex signalling systems. Costs ballooned to £18.9 billion – some £3 billion over budget. (AFP)