American spokesman Casey Norton said the airline did not immediately know the cause of the outage, which began around 11 a.M. CDT and lasted nearly two hours.
Flights on both American and its regional affiliate, American Eagle, were halted.
The Federal Aviation Administration said that American Airlines planes destined for Dallas-Fort Worth International Airport, O'Hare Airport in Chicago and Miami International Airport were held on the ground during the outage.
American did not immediately say how many flights were affected.
Combining technology systems is a difficult feat that has tripped up other airlines, notably leading to several outages at United Airlines after it merged with Continental Airlines in 2010. United suffered two major outages this summer.
American has made meticulous plans to avoid a similar fate. Among other moves, it will reduce flights to lighten the load on its network while it combines the two reservations systems.