The Climate Change Bill has cleared the Commons with a huge majority.
The bill, which was given a third reading by 463 votes to three, commits the government to reducing emissions by 80 per cent by 2050.
Ministers moved to bring greenhouse gas emissions from aviation and shipping into the bill at the last minute following a campaign by backbench MPs and environmental groups.
An early day motion tabled by former minister Nigel Griffiths calling for the change was signed by 97 MPs, including 82 Labour backbenchers.
Announcing the government's U-turn, climate change minister Joan Ruddock said: "International aviation and shipping have long been contentious issues in relation to climate change and the subject of much backbench interest, as illustrated by the huge support for the early day motion tabled by Nigel Griffiths.
"We agree that action to reduce emissions from international aviation and shipping will be vital to global efforts to tackle climate change.
"That is why we are already taking forward a range of measures to reduce the impact of international aviation and shipping on the environment."
International efforts were being made to reach an agreement on how to deal with emissions from shops and planes travelling internationally, she said.
The government has agreed that those emissions should "either be included in the Bill's targets and budgets... or an explanation should be laid before Parliament explaining why this has not been done."
The legislation requires the government to publish five-yearly carbon budgets capping pollution from this year.
The new Climate Change Committee will be told to advise the secretary of state on the consequences of including emissions from international aviation and shipping each time it provides a carbon budget.
The bill makes the UK the first country to sign up to legally-binding national targets for reducing emissions.
Conservative spokesman Gregory Barker said: "While we welcome the fact that the government is going to include emissions from aviation and shipping, the measurements of emissions from the movements of goods and passengers should account for all stages of the journey, rather than just singling out the carbon footprints of flights and sea journeys to and from the UK.
"That way we can avoid such unintended consequences as encouraging more polluting methods of travel outside of the UK."
Liberal Democrat spokesman Steve Webb said of the government's changes: "They are a nudge and wink. But they guarantee nothing.
"Our concerns remain that the guarantees that the nation and the planet seek on the government's attitude to aviation and shipping aren't firm enough."
Dods Parliamentary Communications Ltd