Aris Salonika part company with coach
"Given the conditions, I believe it is right for me to leave the club. I believe it will change things for the best," Hernandez, who took over from Serbian Dusan Bajevic last July for a second spell in charge of the club, said in a statement.
Aris are seventh in the Super League and a 4-0 defeat by Panathinaikos on Saturday effectively sealed Hernandez's fate.
Brazilian Iomar do Nascimento Mazinho is scheduled to arrive in Thessaloniki on Thursday to take over the role of head coach.