The incident was a harsh reminder of police brutality rampant in the nation.
The directorate received 720 new cases for investigation of suspicious deaths in custody or in other policing contexts between April 2011 and March 2012, Amnesty said.
"This appalling incident involving excessive force is the latest in an increasingly disturbing pattern of brutal police conduct in South Africa," said Noel Kututwa, Amnesty International's southern Africa director.
In defense of the police force
But authorities defended officers, saying they are not a reflection of the entire nation's force.
"There are many other officers who are dedicated, who uphold the law and arrest criminals all the time," Dlamini said.
Under apartheid rule in South Africa, white police officers subjected the nation's black majority to inhumane treatment. But in this case, the man and police in the video, as well as those in the crowd, are black.
Apartheid rule ended in the 1990s, and the government reformed the police departments and made them more diverse.
A series of scandals
Despite the changes, the nation grapples with a high crime rate, including rapes, armed robberies and police brutality, analysts say.
South Africa's history of violence "is part and parcel of daily life," said Johan Burger, a senior researcher with the Institute for Security Studies in Pretoria.
Some police officers believe that they "are above the law" and that there won't be consequences for their actions, he said.
South Africa's police force has been plagued by a series of scandals recently.
In August, officers opened fire on striking platinum miners in Marikana, killing 34 in one of the most deadly police shootings since the end of apartheid.
Last month, one of its officers -- Hilton Botha -- was booted from a high-profile murder case after prosecutors reinstated attempted murder charges against him.
He is accused of chasing and firing on a minibus full of people while drunk in 2011. He is charged with seven counts of attempted murder.
Botha was testifying in the trial of Paralympic star Oscar Pistorius, who is charged with killing his girlfriend on Valentine's Day. He later resigned from the force, citing personal reasons.