He was charged with corruption, allegedly having taken bribes and never declaring Swiss bank accounts.
The country's first female president will be removed from office.
The Senate is set to try the president for breaking budget laws on Wednesday.
President Dilma Rousseff is accused of breaking budget laws as the country goes through its worst recession in decades.
Waldir Maranhao said there were procedural flaws in the chamber's vote that accepted the impeachment charges.
The vote is a crucial step towards a potential impeachment.
Now, the full lower house must vote on the impeachment proceedings, which is expected to take place on Sunday.
Dozens of opposition lawmakers also interrupted a session of Congress to call for the president's resignation.
The president is accused of violating Brazil's financial laws.