The Pakistanis, crew of the ship Al-Raymanz, were detained in the central province of Zambezia after the authorities suspected the vessel was carrying illegal cargo or transporting illegal migrants to South Africa.
It was later found that the vessel was not transporting anything illegal.
The ship was held in Quelimane after docking.
The vessel had run out of fuel and the crew members told Radio Mozambique they docked at the harbour in search for food and water.
The Pakistanis spent 21 days at the port even after paying a fine to the provincial maritime services, Zambezia maritime administrator Daniel Sitoi told Xinhua.
"The 11 crew members have left as nothing was suspected to have occurred clandestinely," he said.
Their release was ordered by Mozambican Defence Minister Jacinto Nyusi.
