The BBC's Azizullah Khan in Quetta says Ghullam Muhammad Baloch was a leader of his own faction of the Balochistan National Movement and a key member of the committee set up to try to secure the release of abducted UN worker John Solecki, who was freed last Saturday.
Sher Muhammad Bugti was a leader of the Balochistan Republican Party.
The three were allegedly detained last Friday by security forces from the offices of a lawyer in Turbat who represents opposition parties in Balochistan.
After the bodies were found riots broke out in provincial capital Quetta, Khuzdar and a number of towns in the Makran division.
A number of banks and offices have been set on fire.
In Quetta, three policemen were injured when a grenade was thrown at a police van.
Police and paramilitary forces have been deployed to control the riots and tear gas has been fired at protesters in Quetta.
Police spokesman Ayaz Baloch told the BBC an investigation was under way but it was unclear who carried out the killings.
Balochistan Chief Minister Mohammad Aslam Raisani has ordered a judicial inquiry into the leaders' deaths.
Opposition activists had been demonstrating since the leaders disappeared on Friday, setting up a protest camp outside the press club in Quetta.
In August 2006, Balochistan experienced widespread rioting and strikes after the killing of tribal leader Nawab Akbar Bugti. Hundreds were arrested.
Writing recently on Balochistan, BBC columnist Ahmed Rashid pointed to the worsening situation in the province, where the wide-ranging political and economic grievances of the alienated Baloch people have remained largely forgotten and unaddressed.
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