"Sajad Ahmad Geelani of Pandaan-Nowhatta and Haaris Ahmad Langoo of Gojwara were booked under PSA and sent to Kot Balwal Jail," a police spokesman said.
He said the duo were "die hard" stone pelters and wanted by police.
While six FIRs related to stone-pelting were lodged against 23-year-old Geelani at Khanyar Police station, 19-year-old Langoo was wanted in five similar cases, he said.
The arrest of the two youth led to protests by locals residents in parts of the interior city.
The protesters blocked the roads at Saraf Kadal, Kawdara, Nowhatta and Rajouri Kadal demanding release of the arrested youth, officials said adding some protesters turned violent at Saraf Kadal and Kawdara and indulged in stone pelting but were chased away by police.