Mohamed al-Romaihi scored for the Pearl Divers in the second half of the match held at Abdullah bin Khalifa Stadium.
Salman al-Faraj missed a penalty for the Green Falcons after Salem al-Dawsari was brought down inside the Bahraini penalty box by Mahdi al-Humaidan.
The Saudis were looking to lift the title for the fourth time. During the competition’s group stage, Bahrain had lost 0-2 to Saudi Arabia.
It is the first time that Bahrain have won the title.