The updated scheme, dubbed by some parliamentarians and stakeholders as 'stop the clocks II', has received mixed reactions, with some accusing the revised text of undermining EU climate policy.
Following the vote, Greens/EFA deputy Satu Hassi said, "MEPs have today voted to let most of the aviation sector off the hook for its growing climate change impact in exchange for the vague hope of future global action.
"Excluding international aviation from the emissions trading scheme for four extra years will mean four more years of growth in airline emissions, undermining the emissions reductions from most other EU sectors.
"The original legislation including aviation in the EU's emissions trading scheme covers one third of global aviation emissions; it is reckless to dismantle this effective climate policy instrument in exchange for a vague promise on a global scheme in the distant future without guarantees of environmental integrity or ambition," argued the Finnish MEP.
"The actions of Airbus and the European airlines to undermine EU climate policy have been shameless and discredit the sector as a constructive partner for the future," she concluded.
However, speaking in a press conference following the vote, rapporteur Peter Liese defended his report, describing it as "the best possible compromise" and admitted that though he was "not entirely happy" with the changes to the text, he was pleased that it "keeps the ETS alive for aviation".
He said, "For the environment, this text is not only better than the council position, but also better than the commission proposal.
"The key element for us concerns the scope. The emissions trading system will again apply in full after 2016. Parliament could not accept the council's wish to 'stop the clock' until 2020.
"We have the next international civil aviation organisation (ICAO) assembly in 2016, and if it fails to deliver a global agreement, then nobody could justify our maintaining such an exemption for another four years," added the German deputy.
Parliament's environment, public health and food safety committee chair Matthias Groot was more pessimistic, however, saying, "CO2 emissions are on the rise, while the international civil aviation organisation waits for a global agreement. But time is running out."
"I find the negotiated compromise too weak, but if it may contribute to find a solution for tackling aviation emissions at the global level, fair enough."
Speaking in parliament, he said that it is "now up to civil aviation companies to deliver" and even though "a majority is a majority", he hoped that he would "not see the EU meeting again for stop the clock III or IV".
Meanwhile, environmental NGOs condemned the compromise, with Bill Hemmings, aviation manager at Transport & Environment, saying, "Just when the [intergovernmental panel on climate change]'s latest report shows how climate change is already affecting every aspect of human life, European governments and politicians have chosen to effectively scrap the only law in the world that attempts to curb aviation's soaring emissions."
He continued, "Regulating emissions in European airspace is not only our right, but also our obligation - something those who cried wolf about a 'trade war' seem to have forgotten."
"If no meaningful progress is made in ICAO in 2016, the pressure on decision makers to stand by their promise to revert back to a full aviation ETS will be overwhelming," warned Hemmings.
Jason Anderson, from the WWF European policy office, also expressed disappointment, saying, "A continuation of 'stop the clock' in order to achieve a global agreement in the international civil aviation organisation is making the environment pay the price as aviation emissions coverage in the EU ETS will now be reduced by 75 per cent.
"The EU has compromised too much in pursuit of this aim, with no guarantee of success."
He went on, "What we need to see now is the BRICS, US and other countries to take a more constructive role within ICAO to ensure the adoption of a market-based measure for aviation, ideally one that generates revenue to help developing countries take climate action.
"We also need to see the airline industry continuing to stand firm in their support of global and regional measures to reduce aviation emissions. Only then will the EU's sacrifice not have been in vain."
But, Athar Husain Khan, CEO of the association of European airlines, praised parliament for its "realistic approach which provides clarity for airlines for the next three years", though he added, "We would have preferred legal certainty and planning stability until 2020 when the global market-based mechanism is due to come into force."
"The new scope puts an additional burden on airlines primarily serving intra-European routes, but by amending the aviation ETS, [parliament] has paved the way for further progress at international level.
"AEA fully supports the ICAO process as it is the only way to ensure a global solution for a global problem," he concluded.