The organisation responsible for co-ordinating European air traffic says it has fixed an earlier fault which led to widespread flight delays.
Eurocontrol earlier said that delays could affect up to half of all flights in Europe - about 15,000 trips.
It said the faulty system was restarted at 19:00 GMT, and normal operations had resumed.
Tuesday's fault was only the second failure in 20 years, Eurocontrol said - the last happened in 2001.
The unspecified problem was with the Enhanced Tactical Flow Management System, which helps to manage air traffic by comparing demand and capacity of different air traffic control sectors.
It manages up to 36,000 flights a day. Some 29,500 were scheduled on Tuesday when the fault occurred.
When the system failed, Eurocontrol's contingency plan for a failure in the system deliberately reduced the capacity of the entire European network by 10%. It also added what it calls "predetermined departure intervals" at major airports.
In a statement, the group said it "very much regrets the disruption that has been caused to passengers and airlines due to today's outage."
"We have never had anything like this before," a Eurocontrol spokesman told the AFP news agency.
But air traffic control itself was not directly affected, and Eurocontrol said "safety was not compromised at any time".
Earlier in the day, several European airports had warned passengers to expect delays, with Brussels Airport saying it was limited to just 10 departures every hour. Schiphol in Amsterdam, Helsinki, and Dublin airports also warned passengers about delays of varied lengths.
On Tuesday afternoon, Eurocontrol said its contingency plan would be in place for several hours, "until we are certain that sufficient data is in the system to allow it to operate completely correctly".
Eurocontrol announced the system restart later in the day, after what it called extensive testing.
It also asked airlines to resend any flight plans filed before 10:26 UTC, which it says were lost in the system failure.
Under EU law, passengers on delayed flights are usually entitled to compensation. But an exemption applies if the delay was caused by an "extraordinary circumstance" out of the airline's control.