Nekounam was named as new head coach of Paykan in late December, but General Manager of Iran Khodro Company (IKCO) Hashem Yekezare disagreed with the appointment.
Paykan later appointed Hossein Faraki as its new head coach.
Nekounam, who had stepped down as Nassaji coach earlier, has returned to the Ghaemshahr-based football team once again.
Under guidance of Nekounam, Nassaji won a promotion to the Iran Professional League (IPL) after a 24-year absence.
Nassaji sits 10th in IPL table, 15 points behind leader Sepahan.