The Sabre system, used by more airlines in North America than any other, stopped working for just under three hours.
A spokeswoman for Sabre, which operates online booking systems for airlines including American, Virgin and JetBlue, told CNBC Sabre was experiencing a system issue. The systems were coming back online around 2 a.m ET, however, she said, adding the firm was "closely monitoring" the situation. According to American Airlines' statement, the outage started at 11:45 p.m. ET.
JetBlue warned that it could experience delays after switching back to a manual system following the outage.
American Airlines confirmed that it is "currently experiencing an outage involving its reservations system".
"It's our understanding that other airlines and travel agencies are also impacted by this. We are working with our technology partners to determine a solution," a spokesman for the airline said.