Gatwick was forced to shut its runway when only one air traffic controller (ATC) was available, the airport said.
Several inbound flights were diverted or delayed due to the staff shortage at the West Sussex airport.
Only one controller out of the scheduled three was able to work in the control tower, reportedly due to sickness.
Controllers need to take two one-hour breaks per shift, meaning the runway was closed from 1.40am-3.20am and 4.10am-5.20am on Sunday and Monday - four closures in total.
Two inbound flights were diverted and several were delayed in the early hours of Sunday morning, with a further four delayed on Monday.
There were no scheduled departures during those periods.
Responsibility for air traffic control at Gatwick switched from Nats to Air Navigation Solutions in March 2016.
Gatwick believes the staffing issue has been resolved.
An airport spokesman confirmed the runway closed "due to a shortage of available air traffic controllers during the night shift".
He added: "We worked closely with air traffic controllers and airlines to minimise the impact to passengers. We apologise for the inconvenience caused."