Perez is the outgoing head of the Justice Department's Civil Rights Division.
Holder appeared before the House Judiciary Committee to answer questions about several controversies that have erupted in recent days.
Rep. Darrel Issa, R-Calif., played a recording at the hearing purporting to show Perez offering to withdraw the United States from a whistle-blower suit. Issa is a frequent critic of Perez.
Issa claimed Perez acted inappropriately in getting St. Paul, Minn., city officials to drop a lawsuit seeking to limit fair housing claims when intentional bias is missing -- trading the government withdrawal from the whistle-blower suit for the ending the St. Paul suit.
Issa repeatedly interrupted Holder's long answers to questions, demanding a yes or no.
At one point, Holder refused to stop talking and described Issa's method of questioning as "unacceptable" and "shameful" for a congressman.
A Senate panel was scheduled to hold a hearing on Perez' nomination Thursday.
Republicans on the committee attacked Holder on a number of fronts, from abortion to the investigation of the Boston Marathon bombings.