The bill was the first piece of legislation debated on the House floor after the US Congress returned from recess on 13 November, and had been cleared by the Senate in September in a rare unanimous vote.
It gives the American transportation secretary the power to shield US airlines from Europe's Emissions Trading System (ETS).
Lawyers have said the bill is an unusual piece legislation because it would prevent US companies from complying with the laws of another country.
"It never made a bit of sense for European governments to tax our citizens for flying over our own airspace - and with the passage of this law we've got the tools we need to prevent it from happening and protect American jobs," said Democratic Senator Claire McCaskill, a co-author of the bill.
The House passed the bill despite the announcement on Monday that the European Union would "stop the clock" on enforcing its law for one year.
McCaskill and co-sponsor Republican Senator John Thune said in a statement that their bill had pressured the EU into delaying the enforcement of their cap-and-trade scheme for aviation.
The EU had also been under pressure from China, one of the world's fastest growing markets for aircraft, which had threatened to cancel orders of European Airbus aircraft if the EU did not back down from applying its ETS on all airlines.
One EU official took to the social networking site Twitter to suggest that United States was not making good on suggestions for "greener" policies.
Obama made reference to climate change as one of a trio of issues facing the country in his victory speech after being re-elected on 6 November.
"So far the reelected President Obama climate policies look EXACTLY as in first term. Wonder when we'll see the announced change?" Connie Hedegaard, EU climate action commissioner, said in a tweet.