Andrea Stramaccioni's Panathinaikos went into the match on the back of two successive victories but they were undone in the Northern city of Komotini by Rogerio Martins' 28th-minute goal.
Greece striker Nikos Karelis had hit the woodwork in the first half but, other than a few half-chances, that was the best the visitors could offer against second from bottom Panthrakikos.
"Today's result was a big step back for us," said a deflated Stramaccioni. "I'm not happy at all with the players, clearly some of them had their minds elsewhere and were maybe thinking about the upcoming Christmas holidays.
"There's nothing else to say except that we have to try and keep whatever positives there were from the game and move on quickly."
Olympiakos powered to their 14th win in 14 league matches on Saturday, defeating bottom club Kalloni 2-0 thanks to a double from Kostas Fortounis.
Marco Silva's league leaders now head into the Christmas break well clear at the top.
Third-placed AEK Athens were not in action on Sunday but Gus Poyet's team are one point adrift of Panathinaikos and will leapfrog their city rivals with a win at home to Levadiakos on Monday.
(Editing by Tony Jimenez)
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