Nathan Nandala Mafabi has also retained his seat as Secretary General, running unopposed.
Amuriat secured victory with 800 votes, defeating Moses Byamugisha who received only 187 votes.
The national delegates conference took place on October 6 at the Patidar Samaj Sports Grounds in Lugogo, Kampala.
Out of the 79 nominated candidates, 38 were elected unopposed.
Mukalazi Kibuka, the party vice chairman for the Central region, chaired the conference attended by 1,143 delegates.
Yusuf Nsibambi, elected as the deputy president for Buganda region, replaced Erias Lukwago who now serves as the interim president of the Katonga faction.
Robert Centenary was voted as the vice chairman of the western region, while Jamal Wante became the vice chairperson of the eastern region, succeeding Proscovia Salaam Musumba, among other appointees.
Geoffrey Ekanya will serve a second term as Treasurer General, defeating Lucy Akello Franca. Ekanya secured 626 votes against Akello's 355 votes.
Ajuna Daka was elected National Mobilizer, and John Kikonyogo is the new Party spokesperson.
Jack Sabiiti was elected as the national chairman for the party without any opposition.
Amuriat emphasised that no individual is superior to the FDC constitution, pledging to unite the party as he assumes leadership.
"There can only be one FDC...We will not tolerate two centers of power. If you believe you are above the FDC constitution, then you have no place in FDC," Amuriat declared.
Mafabi disclosed that the party was on the verge of deregistration if they had failed to conduct the National Executive Committee (NEC) elections.
"Katonga is a place for activism. I want to inform the people of Uganda that after tomorrow, we aim to remove those misusing our name in Katonga as FDC. FDC is based in Najjanankumbi, with offices at the district, sub-county, parish, and village levels," Nandala said.
The Katonga faction of FDC failed in their attempt to block the delegates conference organized by the Najjanankumbi faction on Friday.
Wasswa Birigwa, the FDC national chairperson, along with 27 others, sought a court order to stop the Najjanankumbi delegates conference, claiming they would lose their party positions.
They also asked for a temporary injunction to halt the conference and the elections for FDC National Executive Committee members.
However, on Thursday, Justice Musa Ssekaana ruled that the application by Birigwa and the others had no merit and dismissed it.