A retired colonel, Khanzada, 71, was killed on August 17 when two suicide bombers attacked him while he was meeting people at his political office in Attock district of Punjab.
The suspects were arrested by the Counter-Terrorism Department (CTD), which Khanzada helped to set up to counter militancy in the province.
A police official said that the two men belonged to a banned outfit and were shifted to a secret location for interrogation.
The suspects had been following Khanzada over the past couple of weeks before terrorists targeted him in a suicide attack, he added.
The banned outfit Lashkar-e-Jhangvi (LeJ) has reportedly claimed responsibility for the suicide attack on Khanzada, to avenge the killing of LeJ chief Malik Ishaq.