Gunfire and explosions were reported in Quetta and mobs attacked a bank, shops and government offices after the prayer service for the 79-year-old Baloch leader at a sports stadium attended by political and religious leaders.
His body is yet to be recovered from the cave where he was hiding after the Pakistan Army near Dera Bugti district attacked it on Saturday.
Police used teargas shells and fired in the air to control the rampaging crowd on Tuesday. Two people, including a policeman, were injured.
According to reports, Quetta Mayor and member of the ruling PML-Q Mir Maqbool Ehmat Lehri was chased away by Bugti's supporters who shouted slogans like 'Death to Pakistan's Army', 'Pakistan will disintegrate' and 'Pakistan will no longer exist'.
Those who attended the prayers included two of Bugti's sons who are active in his Jmabhoori Watan Party as well as other top Baloch nationalist leaders like Ataullah Mengal and Geir Bux Murri, local TV channels reported.
Police and security forces stayed quite a distance away from the place where the prayers attended by over 10,000 people were held as a military helicopter hovered over, reports said.