"Who gave you the right to judge? Who gave you the stand to address Friday (weekly) prayers and state television?" he said, referring to Hassan Khomeini's failed candidacy for elections to Iran's powerful Assembly of Experts.
"May God forgive you," said Rafsanjani, a veteran of Iranian politics and two-term president, quoted by state news agency IRNA.
"Without Imam (Ruhollah) Khomeini, none of these people (on the vetting panel) would have existed."
Hassan Khomeini, a cleric aged 43 who has ties to reformists in Iran, said Friday he would appeal being barred from running in the polls.
He is among hundreds who have been excluded from elections next month for the assembly, which monitors the work of Iran's supreme leader and has the authority to replace him.
Signup to our newsletter and follow us on Facebook and Twitter!
The Guardian Council, a conservative-dominated panel that decides who can run for public office, said only 166 of 800 candidates were approved.
Khomeini, who failed to attend a qualifying exam, said other candidates had been vetted even without taking the test.
Voting for the 88-member assembly, of which Rafsanjani is a member and for which he is running again, will take place on February 26, the same day as parliamentary polls.
Both elected bodies are dominated by conservatives.
The Guardian Council said last week that 60 percent of 12,000 candidates for the elections to parliament had been excluded. Only one percent of reformist hopefuls won approval.
Iran's incumbent reformist President Hassan Rouhani is hoping for a strong electoral showing by the pro-reform camp to press ahead with his political and social programmes.