Permits to pollute any more than that will have to be bought in an auctioning scheme, or traded in the Emissions Trading Scheme (ETS).
The EU executive estimates that this will save 72 million tonnes of CO2 a year by 2020.
"We are making a fair judgement," said Jos Delbeke, the European Commission's director general for climate action. "We are giving a number of allowances for free to allow airline operators to make their aircraft and operating procedures more environmentally friendly and to reduce the greenhouse gas emissions."
Market analysts Point Carbon say that the Top 10 airlines will be hit hardest by the new scheme, as they face a 30 million-tonne shortfall in their CO2 allowances next year. Consequently, the €360 million bill will then be passed on to the consumer.
"A relatively few large airlines account for a really significant proportion of the scheme," Andreas Arvanitakis, Point Carbon's associate director told EurActiv.
Point Carbon singled out a Top 10 by shortfall in 2012 of: Air France, Alitalia, American Airlines, British Airways, Delta Airlines, Iberia, Lufthansa, Ryanair, United Airlines and Virgin Atlantic Airways.
"About half of the CO2 covered by the scheme will come from the top 30 airlines, and the top 10 alone will account for over a third of all emissions," Arvanitakis said.
That cost would be passed on to the consumer, to the tune of between €2-€12 per flight, according to the EU. Arvanitakis agreed that this was the most likely outcome, but added:"It's a very cost-conscious industry, particularly for the low-cost carriers."
"The flag carriers could pass on more of the cost to business class travellers, where an extra €10 might not make much difference, but on a low cost flight it's more significant," he argued
Free allocations, the unfortunate gift
Environmentalists broadly welcomed the EU's announcement, which will apply to EU and non-EU airlines alike, but bridled at its €2.3 billion "windfall" of free allocations to a fast growing and highly polluting industrial sector.
Sam van den Plas, a policy officer for the World Wildlife Fund called it "an unfortunate gift," but stressed the group's satisfaction that aviation had finally been brought into the ETS.
"This is an implementation of existing European law after more than ten years of inaction under the international body International Civil Aviation Organisation," he told EurActiv. "It is a useful step in the direction of a global approach to tackle emissions."
One airline industry insider bemoaned what he saw as a "weakness" in the lack of precision used in the language over what would be done with auctioning revenues.
"There is some very ambivalent language used and I think the Commission would have liked to have placed an onus on member states to use the revenues for environmental purposes but the states pushed back on that and the language was weakened," the insider added.
Instead of an obligation to reinvest monies raised in environmentally-friendly ways, the Commission only says that it "should" be used to do so, giving rise to doubts.
EurActiv understands that German reservations - that the scheme might distort a global level playing field under article 25a of the existing directive creating an ETS - were resolved at an informal environment minister’s council lunch on June 16.
"A clarification was given that this article should be applied and interpreted in a way that assured us that a global level playing field could be guaranteed," a German diplomat told EurActiv.
Two weeks later, the European Commission issued an updated guidance document that was "designed to create a level playing field between all sectors and installations".
"There was also an understanding that this inclusion of aviation in the ETS is a test for how robust the European approach is to climate policy vis-à-vis our international partners," the diplomat added. "It would be the wrong signal if we started to step back."
The European Court of Justice is currently considering a suit brought by the Air Transport Association of America and American, Continental and United Airlines, which challenges Europe's right to apply ETS regulations to non-EU airlines.
An opinion by the Advocate General on October 6 is expected to give a sense of which way the Court will ultimately rule.
Arvanitakis anticipated "substantial resistance" to the new benchmarks from non-EU registered airlines.
"The mid-ranking and smaller airlines are relatively unprepared and still have a steep curve to climb before the scheme actually starts," he said.
But there was strong qualified support for the new benchmark scheme from the European Low fares Airline Association (ELFAA).
"We see in the inclusion of the aviation in the ETS the environmentally best and most worthwhile way of reducing aviation emissions that offers any payback to the environment," said John Hanlon, ELFAA's secretary general.
But, he added, "in the low fares market, if you could charge customers €12 more for a flight, I don't think that we would be waiting for the introduction of the ETS."
As a fast growing sector since 2006, he said he also anticipated low cost airlines taking a hit from the new rules.