The Agus-Sylviana pair left the Democratic Party office at 19:00 hours local time.
The duo, sporting the traditional attire of Betawi, arrived at the Jakarta General Elections Commission offices at 19:45 hours local time.
They were welcomed upon their arrival by their supporters who performed qasidah (Arabic music), and said shalawat (prayers to Prophet Muhammad).
The son of former President Susilo Bambang Yudhoyono, Agus Harimurti Yudhoyono, a major in the Army, was earlier named candidate to contest the next Jakarta gubernatorial election in 2017.
Deputy Jakarta governor for tourism and culture, Sylviana Murni, will be Agus running mate, nominated by the coalition of Democratic Party, the United Development Party (PPP), the National Awakening Party (PKB) and the National Mandate Party (PAN).
Both the names came as a surprise for most observers. These names emerged only during a series of meetings among the four minority parties at Yudhoyonos residence in Cikeas, Bogor, West Java.
"It was agreed that the candidate for the posts of governor and vice governor, which will go to polls in 2017 will be Agus Harimurti Yudhoyono and Ms Sylviana Murni," Zulkifli Hasan declared after one such meeting in the early hours of Friday.
PKB General Chairman Muhaimin Iskandar said the decision to name Agus and Sylviana was based on a number of factors, and was in the interest of the people of Jakarta.
"A combination of a young and fresh man with high integrity, and a career civil servant, is promising," Muhaimin added.
Agus Harimurti Yudhoyono will end his military career and Sylviana will have to tender her resignation as a civil servant to be able to take part in the election to challenge the incumbent pair of Basuki Tjahaja Purnama (Ahok) and Djarot, who are contesting again.
The pair of Ahok-Djarot has been nominated by the ruling Indonesian Democratic Party of Struggle (PDIP), the NasDem, the Hanura and the Golkar Party.
Another pair is expected to be announced by the coalition of Gerindra and PKS on Friday, the last day for officially registering with the Election Commission.
Ahok-Djarot has so far topped all voters polls against other potential candidates and pairs, but the pair of Agus-Sylvian was not included in any of those polls.