The announcement was made while the Crown Prince was leaving Indonesia, after the G20 summit.
The centre covers 109,435 square metres with facilities including a mosque with an area of 2,200 square metres, which accommodates more than 20,000 worshippers, a research studies centre and a conference hall.
The large dome of the mosque collapsed in October during its renovation after a major fire, without causing any casualties.
The gesture “stresses his keenness and concern in Islamic centres in all brotherly and friendly countries, for their big role in raising future generations and spreading tolerance of Islam and message based on peace, moderation and dialogue”, the Saudi Press Agency reported.
Sheikh Dr Abdulrahman Al Sudais, General President of the Grand Mosque and the Prophet's Mosque Affairs, praised the decision.
“Since the establishment of the kingdom, its rulers have taken care of buildings and building mosques, and Indonesia is at the forefront of countries that have received the support of the kingdom in this field, as it is the largest Islamic country in terms of population,” he said.
Prince Mohammed sent a cable of thanks to Indonesian President Joko Widodo following his participation at the G20 summit on Wednesday.
The Saudi Crown Prince congratulated him on successfully hosting the summit.
"The positive results we have reached during your presidency, stress the importance of the decisions issued by it, which we hope will contribute significantly to supporting cooperation among the countries of the group and enhancing the growth rates of the global economy," he said.