The 24-year-old, who was Zamalek's top scorer in the Egyptian league with nine goals as his side finished runners up to champions Ahli, scored on 68 minutes to end the resistance of Fayoum.
The Cairo side avoided last season's nightmare scenario when they bowed out at the first hurdle after losing 1-0 to third-tier Bani Obeid.
They are now expected to meet arch-rivals Ahli, who face Nabaroh later in the day, in the Egyptian Cup round of 16 on Wednesday.
Zamalek struggled to threaten Fayoum goalkeeper in the first half, with their forwards unable to hold off challengers.
Gaafar and attacking midfielders Alaa Ali, Shikabala and Ivorian Remi Adiko could not carve out space for themselves against a resilient Fayoum side, who wasted a golden opportunity to stun the visitors.
On 30 minutes, Fayoum's Farag Abdul-Mohsen rose unmarked to head a corner goalwards but Zamalek keeper Abdul-Wahed Al-Sayed superbly tipped the ball onto the bar.
Bizarre Incident
Zamalek continued to pass the ball aimlessly in the early minutes of the second half before coach Hossam Hassan made the difference after introducing winger Hussein Yasser.
Yasser replaced the ineffective Adiko, who recently expressed his delight at returning to Zamalek's fold after a long absence but hardly repaid Hassan's faith.
It was a neat move from Yasser which helped Gaafar break the deadlock eight minutes past the hour mark.
He evaded a defender on the right and whipped in a pinpoint cross for the towering Gaafar to head home.
The match was halted for several minutes shortly after following a bizarre incident in the stands.
TV cameras caught Zamalek fans hurling stones at people standing in the balconies of nearby buildings. Security forces eventually intervened to end the matter.
Fayoum could have scored a shocking equalizer deep in stoppage time but once again Al-Sayed, one of Zamalek's most consistent performers this season, came to their rescue.
He dived full stretch to block Mohamed Hassan's low shot from the edge of the area.
نرشح لكم
الزمالك يتلقى دعوة من الإفريقي التونسي لإقامة وديتين احتفالا بالتتويج بالدوري
"بداعي الإساءة لجماهير المصري".. الأعلى للإعلام يعلن تلقيه شكوى ضد أحمد شوبير
أحمد حجازي يتبرع بـ 200 ألف جنيه ضمن لنادي الإسماعيلي لحل قضاياه الدولية
"موقفكم يؤكد أن الكرة أخلاق أولا".. حارس مرمى إنبي يشكر جماهير المصري
"حققت كل ما جئت لأجله".. رسالة أليو ديانج بعد رحيله عن الأهلي
خبر في الجول - بيراميدز يتمم اتفاقه لضم خالد عوض
الأهلي يعلن رحيل أليو ديانج
بعد الرعاية التاريخية.. هيثم عبد العظيم يكشف لـ في الجول رؤية أورا لدعم الكرة المصرية












للمرة الأولى في التاريخ.. لاعب من الدوري السعودي يفتتح أهداف كأس العالم
مباشر كأس العالم - المكسيك (1)-(0) جنوب إفريقيا.. القائم يمنع الثاني