Panathinaikos dropped points in a 1-1 draw at home with Larissa on Saturday and are second in the league, level on points with Olympiakos who have played a game less.
The Athens club have performed poorly this season at home and in Europe. In the Champions League Panathinaikos have managed only two draws in four matches.
Nioplias is the former Greece under-21 coach and had been in the job 11 months.
The club announced that 71-year-old Pole Jacek Gmoch, who has coached in Greece including Panathinakos in 1983-1985, will lead the club until a new coach is found.
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