The other three countries being taken to court, Hungary, Italy and Romania, are being referred over particulate matter levels.
The European Environment Commissioner, Karmenu Vella, said the EU "owed it to its citizens", to take legal action.
The commission said that Britain had broken limits for nitrogen dioxide, largely produced by diesel vehicles, and had failed to provide "credible, effective and timely" plans to cut pollution.
The Toxicity Charge introduced in October 2017 in Central London was one of the UK's air quality measures deemed insufficient by the European Commission, given that 16 air quality zones across the nation exceeded the limit in 2016.
The European court of justice (ECJ) has the power to impose multimillion euro fines if the countries do not address the problem swiftly.
"We will shortly build on our £3.5bn plan to tackle roadside emissions with a comprehensive Clean Air Strategy setting out a wide range of actions to reduce pollution from all sources".
The World Health Organisation's director of public health, Dr Maria Neira, said new urgency was need to tackle air pollution: "While air pollution knows no borders and puts everyone at risk, those most vulnerable - pregnant women, children, the elderly, those already ill or poor- are particularly affected".
The European Commission is taking the British Government to court for breaching EU air quality rules. Air pollution requires urgent action and it's been clear for too many years that authorities all across Europe are failing to protect their people from illegal and harmful levels of air pollution.
The EU Commission is also issuing additional letters of formal notice to Germany, Italy, Luxembourg, and the United Kingdom warning them that they have disregarded EU vehicle type approval rules.
Air pollution from NO2 causes an estimated 23,500 early deaths every year in the UK. The Commission should have made no exceptions and referred them all. But Vella also admitted that "legal action alone will not solve the problem".
European Union judges in Luxembourg will be able to hit Britain with huge fines under the bloc' "infringement proceedings".
Internal Market, Industry, Entrepreneurship and SMEs Commissioner Elżbieta Bieńkowska underlined the role that Europe's vehicle industry has in fighting urban pollution. "Manufacturers that keep disregarding the law have to bear the consequences of their wrongdoing".