The duo were already under judicial custody in another alleged fake encounter case of Sadik Jamal.
The arrests came close on the heels of the investigating agency picking up SP (Crime Records Bureau) Girish Singhal on Thursday in this connection.
While JG Parmar, who retired as DSP and also the complainant in the encounter case, was apprehended last night, Tarun Barot, currently Mehsana Deputy Superintendent of Police was picked up this afternoon, sources said on Saturday.
Parmar and Barot, who was then police inspector, were part of the two teams that eventually gunned down Ishrat Jahan and three others riding in a car.
Sources said, Parmar and Barot were placed under arrest after CBI secured a transfer warrant from court in this regard.
Ishrat, who hailed from Mumbra in Thane district neighbouring Mumbai, along with her accomplices Pranesh Pillai alias Javed Sheikh, Zeeshan Johar and Amjad Ali Rana, was killed allegedly in a staged encounter by police on a deserted stretch between Ahmedabad and Gandhinagar on June 15, 2004.
Police had claimed that Ishrat and three others were on the mission to assassinate chief minister Narendra Modi.
With the arrest of the duo, the number of policemen arrested in the case so far has gone up to three.
Meanwhile, a CBI court on Saturday rejected the agency's application seeking 14 days' remand of Parmar and sent him to judicial custody.
Seeking his remand, CBI counsel Ejaz Khan told the court that the offence was grievous in nature and custodial interrogation is extremely necessary for the investigation into the encounter case.
The CBI further said that the complicity and involvement of the accused is revealed in the offence committed, which mandates further detailed investigation.
Parmar's counsel Sanjay Thakkar argued that probe into the case has been going on for two years and he had already been interrogated more than once.
Taking into account both the versions, CBI judge AU Jujara rejected the remand application on the ground that the accused had already been interrogated once.
The agency's plea seeking 14-day remand of Singhal was also rejected by the court.
An SIT, constituted by the Gujarat High Court on the application of Ishrat's mother, had concluded that the teenage girl was killed in a fake encounter.
Following the report, the high court handed over the case to the CBI on December 1, 2011, and has been monitoring the investigations.