El Idrissi crossed the finish line in a brilliant 2h 48min 36sec, beating the previous world best (2h 54min 13sec).
Her countrywoman Meryem En-Nourhi came second (2:58.18), followed by Spanish Elena Congost (3:00.48).
In the men's Marathon T12, Moroccan El Amin Chentouf, the defending champion, settled for the bronze medal, after finishing 3rd with a time of 2h 24min 35sec, his best time this season.
Tunisian Wajdi Boukhili won the gold medal in 2:22.05, ahead of Spaniard Alberto Suárez Laso (2:24.02).
This brings Morocco's haul to a record 15 medals, (3 gold, 6 silver and 6 bronze medals).
Fatima Ezzahra El Idrissi, Aymane El Haddaoui in the 400m (T47) and Mouncef Bouja in the 400m (T12) won the gold medals.
Fatima Zahra El Idrissi in the 1500m (T13), Abdelilah Gani (F53) in the shot put, Youssra Karim in the discus throw (F41), Azddine Nouiri in the shot put (T34), Ayoub Sadni in the 400m (T47) and Meryem En-Nourhi in the marathon (T12) won silver medals, while El Amin Chentouf in the marathon (T12), Aymane El Haddaoui in the 100m competition (T47), Ayoub Adouich (-63 kg/K44) and Rajae Akermach (+65 kg/K44) in para-taekwondo, Saida Amoudi in the shot put (F34) and Azeddine Nouiri in the shot put (F34) got the bronze medals.