Both Glasgow and Edinburgh said flights were back to schedule by 19:00.
A technical issue had caused delays to flights through all of Scotland's main airports.
Edinburgh, Glasgow, Aberdeen and Prestwick airports were affected by the incident at the Scottish Air Traffic Control centre at Prestwick.
Air traffic controllers Nats said there had been interference with some radio frequencies used to talk to aircraft.
The organisation has apologised to passengers and said it was also doing everything it could to safeguard the evening rush hour.
Nats said the faulty piece of equipment had now been removed from service.
All flights at Edinburgh Airport were delayed while three Glasgow Airport flights were cancelled  - one to Gatwick and two to Amsterdam -  and delays were expected throughout the day.
There were also a small number of delays on southbound flights from Aberdeen Airport.
Nats spokesman Paul Haskins told BBC Radio's Good Morning Scotland programme: "We've had a technical problem overnight with interference with some of our radio frequencies which we use to speak to aircraft.
"It only affects some parts of Scottish airspace and flights from and to some Scottish airports but there may be delays as a result this morning.
"We have identified the cause and isolated the problem and the situation is now improving."
Transport minister Derek Mackay said: "There was a technical issue that has been rectified and addressed, however there are knock-on consequences to the airlines.
"People should check with their airlines and the airports to ensure that their flights are running."
Scotland's busiest airports have returned to normal after a day of disruption caused by an air traffic control failure.