Pilot David Paul Allsop was arrested Wednesday morning at Savannah Hilton Head Airport, police said.
Allsop has been charged with driving under the influence, according to an arrest report.
The flight Allsop was supposed to be a pilot for was delayed from 6:05 a.m. to 10:56 a.m. while Southwest searched for a new pilot, officials said.
"We're aware of a situation involving an Employee on Flight 3772 this morning from Savannah," Southwest Airlines said in a statement. "The Employee has been removed from duty. Customers were accommodated on other flights, and we apologize for the disruption to their travel plans. There's nothing more important to Southwest than the Safety of our Employees and Customers."
According to the Federal Aviation Administration, "Regulations prohibit pilots from using alcohol while on duty or flying, or attempting to fly, an aircraft within 8 hours of consuming alcohol or if their blood alcohol concentration of 0.04% or greater."
ABC News has reached out to local authorities for more information about the arrest.
Allsop's bail has been set for $3,500.