Airlines argued that passengers abused the system by bringing a menagerie of animals on board under the guise of "emotional support" including cats, turtles, pot-bellied pigs and, in one case, a peacock.
The Transportation Department issued a final rule Wednesday covering animals on airlines.
It decided that only dogs can fly as service animals, and companions that passengers use for emotional support don't count.
The rule aims to settle years of tension between airlines and passengers who bring their pets on board for free by saying they need them for emotional help.
Under a longstanding department policy, all the passengers needed was a note from a health professional.
The agency said Wednesday that it was rewriting the rules partly because passengers carrying unusual animals on board "eroded the public trust in legitimate service animals."
It also cited the increasing frequency of people "fraudulently representing their pets as service animals," and a rise in misbehaviour by emotional-support animals, ranging from peeing on the carpet to biting other passengers.
The Transportation Department proposed the new rule back in January and received more than 15,000 comments.
While 3,000 commenters favoured dropping protections for support animals, 6,000 spoke in favour of them, including people suffering from depression, anxiety, and post-traumatic stress disorder, the department said.
The Paralysed Veterans of America said the mere presence of a dog, cat or rabbit — even if untrained — can help some travellers, and pet fees of up to $175 (£130 ) one-way are a hardship on low-income people.
The new rule will force passengers with support animals to check them into the cargo hold — and pay a pet fee — or leave them at home.
The agency estimated that airlines will gain up to $59.6 million (£45 million) a year in pet fees.
The number of animals on planes took off several years ago, and a cottage industry grew around providing papers, doctor's notes and even dog vests for support animals.
Delta Air Lines says it carried about 250,000 animals including service dogs in 2017 and about 600,000 last year.
Under the final rule, which takes effect in 30 days, a service animal is a dog trained to help a person with a physical or psychiatric disability.
Advocates for veterans and others had pushed for inclusion of psychiatric service dogs.