Aljazeera's correspondent in Quetta, capital of Baluchistan province, said the clashes occurred after the ceremony for Nawab Akbar Bugti, who was killed in a military assault on a mountain hideout on Saturday, sparking two days of violent riots.
Thousands of people attended the funeral prayers on Tuesday and police had ringed the stadium and troops were on alert, witnesses said.
Police opened fire to disperse the crowd after they began to protest against the killing, Aljazeera's correspondent said.
Meanwhile, representatives of the Islamic League party resigned from the national assembly and regional parliaments to protest against the killing of Bugti.
"It is a big tragedy. Bugti has become a legend," 22-year-old clan member Dad Mohammad said.
"He fought for the rights of ethnic Baluch. He had set a course for the Baluchis - it is now up to the people," said another tribesman, Slaim Shahwani, 25.
Bugti, who was in his eighties, was a controversial but powerful figure who dominated Baluch politics for decades.
Bugti was killed in a military
assault on a mountain hideout
He led a campaign for greater Baluch control over the region's gas resources, and his insurgency which began in 2004 left hundreds of people dead.
He had been accused of running a feudal justice system complete with private jails, and had also been blamed for the deaths of scores of police and soldiers.
More than 500 people were arrested and two people died in the violence over two days, which saw mobs ransack and torch buildings, and a general strike called by Baluch nationalists.
The city was tense on Tuesday and shops were closed in mourning.
Traffic was thin as a heavy police presence patrolled main roads and security was beefed up at government installations.
Mourners coming in groups included tribal elders, former ministers and former provincial governors.
Bugti's body has not yet been recovered from the cave which collapsed during a heavy exchange of fire between security forces and his armed men, officials said.
Efforts were ongoing to retrieve the body for burial in his ancestral graveyard.
Agha Shahid, a senator and Bugti's son-in-law, said that the family approached the ruling party for help in getting the body but that so far there had been no response.
Analysts have described the killing of Bugti as a blunder by the government and have warned it could intensify the insurgency.