"I laud participants, consisting of Muslim scholars, Islamic leaders, and others for performing the mass prayer in an orderly manner," Jokowi told hundreds of thousands of people gathered for the mass prayer.
The president praised the participants, who prayed for the safety of the nation and the state.
On the occasion, the president shouted "Allahu Akbar (God is Great), Allahu Akbar, Allahu Akbar."
In response, the crowd chanted: "Allahu Akbar (God is Great), Allahu Akbar, Allahu Akbar."
In addition, the president called on people to return to their respective places of origin.
After finishing his speech, the president returned to the Presidential Palace on foot, accompanied by Vice President Jusuf Kalla and a number of officials and ministers.
Earlier, Indonesian Police Chief General Tito Karnavian called on the people to support the legal process against non-active Jakarta Governor Basuki Tjahaja Purnama, widely known as Ahok, for alleged religious blasphemy.
"I need your support," Tito told thousands of mass prayer participants at the Monas Square on Friday.
The police chief asked the public to pray for a smooth legal process against Ahok.
"Let us pray together that the legal process can be continued. We will guard (the process)," he added.
The December 2 mass prayer began at 8 am in the National Monument complex with mass Friday prayers as the main agenda.
Some participants arrived at the square since last night, while many others flocked to Istiqlal Mosque overnight on Thursday.