Covic was nominated by the party presidency at his own insistence.
According to a press release, Covic received 283 of 544 votes. The other candidate, Bozo Ljubic, who was nominated by the party's Sarajevo branch, received 258 votes.
Former party president Barisa Colak, who was nominated by the HDZ BiH Western Herzegovina branch, scrapped his nomination before the vote, saying his decision was the result of criticism voiced today to the effect that he had poorly led the party.
The fourth candidate, Ivan Madunic, scrapped his candidacy too, urging his supporters to vote for Ljubic.
After the election, Covic called on the other three candidates and all who did not vote for him to join him in working for the party's benefit.
He also addressed the leader of the delegation of Croatia's HDZ, Luka Bebic, saying that without Croatia's assistance "we can't do anything in Bosnia-Herzegovina".
Bebic said earlier today that the HDZ BiH's policy would not be led in Zagreb, but in Sarajevo and Mostar.
During today's assembly, Covic was sometimes vehemently criticised, with those against his election saying it was bad for the party to be led by a man indicted for corruption. Before the vote, Covic said he was surprised by the harsh criticism.
Earlier today, the assembly heard a letter from the president of the European People's Party (EPP), Wilfred Martens, read by his envoy Wolfgang Grosruck, in which Martens said that the assembly was crucial for the HDZ BiH's future.
The HDZ BiH has applied for membership in the EPP, in which it has observer status since last autumn.
Martens said in the letter there were some people undermining the HDZ BiH's efforts, alluding to Covic. He also said that the HDZ BiH and the EPP must continue Europeanising Bosnia and that the EPP had a reputation for overcoming big obstacles.
Martens added that Bosnia would soon be at the EU's doors when Croatia became the Union's 28th member.
Later today, the HDZ BiH elected party bodies.