The 29-year-old captain was terminated Monday night after the completion of an investigation by the Phoenix-based airline, said Brian Gillman, vice president and general counsel for the company.
"We have a very strict zero tolerance policy," he said.
The first officer and a flight attendant were also tested and those results were negative, Gillman said. The first officer was suspended, and he is under investigation, but the flight attendant has left the company because of a prior resignation, he said.
Security officials contacted Mesa when one of the screeners detected what smelled like alcohol as the crew arrived for the flight. The airline had the crew tested in Little Rock and then flown back to Phoenix during the weekend, Gillman said.
The Federal Aviation Administration is investigating the incident, according to FAA spokesman John Clabes in Oklahoma City.
In an incident in Miami last month, two America West pilots were removed from their plane after screeners said they smelled alcohol. The pilots pleaded innocent to charges of being drunk while operating an aircraft and face a trial in October.