The federal agency announced on Thursday that emergency orders taking away the licenses are effective immediately.
Federal regulations prohibit pilots from operating an aircraft or performing other safety-sensitive functions within eight hours of consuming alcohol or if they have an alcohol concentration of 0.04 or higher, said FAA spokeswoman Laura Brown. America West's policy is 12 hours.
Wednesday, America West (AWA.N) said it was firing the pilots. They can appeal under their union contract.
The decision to fire them was made after authorities in Florida reported that "there was indeed alcohol in their system, in clear violation of (company) policy which is zero tolerance for alcohol use," America West spokeswoman Patty Nowack said.
Police said breath tests revealed the two pilots had blood-alcohol levels above 0.08 percent.
After a security screener noticed they smelled of alcohol Monday morning, pilot Thomas Porter Cloyd, 44, and co-pilot Christopher Hughes, 41, were ordered to return to the gate with their plane and 124 passengers.
Hughes initially told police it was "merely mouthwash," according to police reports.
The two pilots were charged with a felony count of operating an aircraft under the influence and operating a motor vehicle under the influence. They were released on $7,000 bond each late Monday and returned to their Arizona homes.
Arraignment was set for July 22. The pilots could face five years in prison if convicted.
Brown has said Cloyd and Hughes will be able to reapply for licenses after a year by meeting the same requirements they faced when they first applied.
A spokesman for Cloyd's family, Steve Hicks said, "We're saddened by the occurrences and the allegations made against them."
Arizona police records show that Cloyd has been arrested twice for alleged alcohol-related offenses while at his home in Arizona He was sentenced to two years' probation in connection with one incident and took an anger-management class in connection with the other.