The 42-year-old, who took over in September and was in charge for only 19 games, resigned after Wednesday's 2-1 defeat at leaders Olympiakos Piraeus left his side ninth in the table.
"Atromitos would like to thank Ricardo Sa Pinto for his collaboration with the team and we wish him good luck in his coaching career," the club said in a statement on Thursday.
Angelos Anastasiadis also offered to quit as coach of Super League rivals PAOK Salonika on Thursday but it is unclear if his resignation will be accepted by the third-placed team.
(Writing by Graham Wood, editing by Tony Jimenez)
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