The eight-year deal, worth an estimated £150 million a year, is thought to be the most valuable out-of-home ad contract in Europe and has been expanded to include the Docklands Light Railway, London Overground and the new Crossrail line.
Exterion Media was the incumbent but JCDecaux had become a growing presence in London after winning TfL’s bus shelters contract from Clear Channel last year.
TfL promised advertisers that its new deal with Exterion Media will mean greater use of digital technology so ad campaigns can be targeted by time of day and location.
Graeme Craig, the director of commercial development at TfL, said: "We had highly competitive bids from the leading outdoor advertising companies in the world, reflecting the quality and value of our estate. We are delighted to be able to confirm that Exterion Media is our new media partner.
"We believe this partnership can be a catalyst for transforming our stations and the wider industry. The new contract will move away from the traditional concessionary approach to working together to deliver innovation and value on the best station network in the greatest city in the world."
Shaun Gregory, chief executive of Exterion Media, said: "This is a ground-breaking new partnership and together with TfL, we have a bold vision for the London Rail and Underground estate that will transform the look and feel of advertising in the Capital, and the way that brands engage with consumers.
"We look forward to making this vision a reality using our expansive industry expertise, advanced data and insights, and our innovative network of partners, all of which has contributed to making this one of the best monetised, and most valuable advertising contracts in the world."
TfL added: "Advertising is constantly evolving and the new partnership will see the installation of responsive digital screens, which will be able to carry different campaigns according to the time of day enabling advertisers to target their campaigns more effectively."
TfL made the decision at a board meeting, which Boris Johnson, the Mayor of London, was due to chair. The new contract is due to begin in October.
Exterion Media's victory is likely to have significant impact because its owner, Platinum Private Equity, is now in a strong position to exit or merge the business.
Clear Channel and Ocean Outdoor are two other leading players which are owned by private equity companies which may look to consolidate or merge.
Observers said a victory for JCDecaux, the world's biggest outdoor company, would have been more dramatic as it would have had close to 50 per cent of the UK outdoor market and left Exterion Media in a weak position.