Scepovic, playing in his seventh game this season, saw all his three shots at goal find the net, in the 42nd, 52nd and 88th minutes of the Saturday encounter.
Paulo Machado had opened the scoring in the 39th.
Olympiakos remains undefeated after 26 rounds, 23 points ahead of PAOK, which hosts Panthrakikos on Sunday.
The bad news for Olympiakos is that Scepovic is not eligible to play in Tuesday's Champions league round of 16 first-leg home game against Manchester United.
Worse still, veteran striker Javier Saviola, whom Scepovic replaced in the 33rd, has injured his left thigh and is doubtful for Tuesday.
Also, Levadiakos beat Asteras 3-1 and Panionios won 2-1 at Apollon.
