The president arrived at around 09:50 local time with his wife, Iriana Jokowi, along with a group of officials, including East Java Governor Khofifah Indar Parawansa.
Access to the location had been earlier closed by officers, with road closures in place at a number of points.
Jokowi and his group were welcomed by Kyai Haji Miftahul Akhyar, accompanied by a prayer.
Jokowi wore a gray suit and white shirt, while the First Lady wore a purple dress and a veil of the same color.
Kyai Haji Miftahul Akhyar acted as guardian of the marriage, while the marriage sermon was delivered by Habib Hasan Bin Muhammad Assegaf, and the prayer series was read by Kyai Haji Ali Masyhuri, Kyai Haji Anwar Mansyur and Kyai Haji Ubaidillah Faqih.
The reception was also held at the boarding school complex, and only those with invitations were allowed to enter and congratulate the bride and families.
Muktafiyah Bikanafillah, daughter of Kyai Haji Miftahul Akhyar, married her partner, Muhammad Ismail Al Ascoli, who is the great-grandson of the ulema from Bangkalan, Kyai Haji Kholil.
After the reception, the president greeted the crowds of people who had been waiting, and stood for pictures with members of the crowd.
He also visited East Java to hand over land certificates in Gresik District.
Head of the Gresik National Land Agency (BPN), Asep Heri, said that thousands of certificates were distributed in five sub-districts covering 18 villages, including Bungah, Ujungpangkah, Panceng, Wringinanom and Duduksampeyan.
The agency plans to issue 53 thousand more land certificates in 2019.