Flights resumed after being grounded between 12:00 and 4:00 p.m. (0900-1300 GMT), when air traffic controllers joined the protest called by labor unions GSEE and ADEDY.
The government this week issued an emergency order to force high school teachers to work through the May 17-31 university entrance exams and cancel plans for rolling strikes. It was the third time the conservative-led government used the emergency civil mobilization order to end a strike this year.
The government is pursuing unpopular budget cuts to reduce debt as a condition of its international rescue package. It claims it will be able to return to borrowing on bond markets next year, when it also hopes the country's crippling recession will end.
Greece's bond market borrowing rates this week dropped to their lowest levels since 2010, when the country lost market access and was bailed out by its euro partners and the International Monetary Fund.
Interest rates on the 10-year bonds tumbled to below 9 percent, from levels of more than 35 percent last year, after Fitch ratings agency upgraded Greece's sovereign credit rate by one notch on Tuesday.
On Thursday, Fitch also upgraded the ratings of National Bank of Greece, Piraeus Bank, Alpha Bank and Eurobank, citing the lenders' ability to raise money and the country's more stable economic environment.