The intended commercial airport, Branson Airport, was located seven miles south.
To make matters worse, the Boeing 737 touched down on a runway at M. Graham Clark Downtown Airport that was half the size of its intended destination.
One passenger said the landing was abrupt and the pilot applied the brakes really hard.
Scott Schieffer told ABC News that he could smell burning rubber from the plane's tires as they came to a halt.
"The brakes were applied forcefully. We were lurched forward a little bit. I was glad I had my seatbelt on in that case," said Schieffer.
Luckily, no one was hurt. Those aboard the flight which took off at Chicago's Midway International Airport were left wondering as the airport's spokesman Brad Hawkins attempted to spin the incident.
The pilot also spoke to passengers over the intercom after the landing.
"People know we are here and will be taking care of you just as soon as we can," the pilot said, as recorded by a passenger on the plane. "Thanks again for your patience and I apologize."
The airline passengers then took buses to the right airport.
Southwest Airlines released the following statement Monday: "We continue to look into all of the circumstances which led the Captain in command of flight 4013 from Chicago Midway to land at the airport, several miles from the Branson Airport we serve. We want to thank first responders and Branson airport administrators for joining in the work our ground operations staff immediately began to take care of our Customers and their baggage last night and have since reached to each of them directly to apologize, explain what we know, refund their tickets, and provide future travel credit as a gesture of goodwill for the inconvenience."
The Federal Aviation Administration and National Transportation Safety Board are investigating the incident, which marks the second time in less than two months that a large jet landed at the wrong airport.
NTSB investigators say the flight data recorder and cockpit voice recorder from the airplane have been secured and are being brought back to Washington D.C. for readout and analysis. Investigators also plan to conduct interviews with the Southwest Airlines crew this week.
The pilot has been removed from active duty pending the investigation.
ABC News contributed to this report.