Players from rival clubs AEL Larissa and Acharnaikos sat on the field and observed two minutes of silence after kickoff Friday in a game in the central city of Larissa.
AEL said in a statement that the protest was "in memory of the hundreds of children that perish every day because of the heinous apathy of the EU and Turkey about what is happening in the Aegean Sea."
Despite wintry conditions, thousands of people fleeing war and poverty in the Middle East, Asia and Africa continue to risk their lives crossing the Mediterranean to Europe in rickety boats.
At least 33 migrants drowned on Saturday when their boat sank in the Aegean Sea en route from Turkey to Greece, Turkey's Anatolia news agency reported.
The UN says more than 46,000 migrants have arrived in Greece so far this year, with 200 people dying during the voyage.
Last year, Greece received over 850,000 arrivals.
The European Commission on Wednesday hit out at Athens, saying it had "seriously neglected" its duty to protect the bloc's frontiers.