When Ahli sacked coach Hossam Al-Badri, reports said Mokhtar was one of the candidates to take up the vacant seat but Masri quickly dismissed the rumors and issued a hands-off warning over him.
However, Masri's stunning 3-1 defeat by promoted Smouha, who recorded their maiden Egyptian Premier League victory on Thursday, prompted some of the home fans to chant against Mokhtar and call for his departure.
He decided to step down following the team's second successive league defeat despite an otherwise fine league run for the usually mid-table side.
Masri assistant coach Hani Al-Okabi said in a television interview that Mokhtar, who was unavailable for comment after switching off his cell phone before reportedly going to Cairo, would no longer remain in his post, hinting at lack of support from the club's board.
None of Masri's officials, including big-spending chairman Kamel Abou-Ali, commented on the matter.
Mokhtar took over at the Port Said-based club in the summer after leaving Petrojet, the club where he enjoyed great success during the past five years.
Masri, who strengthened their squad with several close-season additions, caught the eye with some impressive displays under the 56-year-old boss.
They displayed attractive football to hold heavyweights Ahli to a draw, beat Ismaili and slump to a cruel loss to Zamalek that came in stoppage time.
Mokhtar left Masri in seventh place with 16 points from 12 games, just three behind fourth-placed Ismaili.
He became the eighth Egyptian coach to depart this season after Mohsen Saleh, Patrice Neveu (Smouha), Ismail Youssef (Gouna), Hossam Al-Badri (Ahli), Hamza Al-Gamal, Mohamed Amer (Arab Contractors) and Carlos Cabral (Ittihad).