The conference had to elect a new leader to succeed Dogan, who is one of the Balkan country's most influential political figures. The 58-year-old has been at the helm of the party since founding it in 1990.
Lyutvi Mestan, who was expected to become the new party leader, said "the true reason for the assault was the language of hatred and confrontation."
Saturday's assault was the gravest attack on a politician in post-communist Bulgaria after the 1996 killing of ex-Prime Minister Andrei Lukanov.
The German government's human rights commissioner, Markus Loening, was at the party caucus in Sofia on Saturday, and witnessed the incident, the German Foreign Ministry said. "I am very happy that Ahmed Dogan was not injured," Loening said in a statement. "Political violence must never again gain a foothold in Europe."