Fatima Tagnaout (11th) and Ibtissam Jraidi (16th, 20th and 22nd) scored for the Atlas Lionesses, while Salma Zemzem (58th) scored the only goal for the Tunisians.
In the first leg, held last Friday in Tunis, Morocco bested Tunisia 2-1.
During the fourth and final round of 2024 Olympic Games qualifiers, Morocco will play Zambia to clinch their ticket for the 2024 Olympics as one of the two representatives of Africa.