His comments were played repeatedly on Pakistani television channels.
Prime Minister Yousuf Raza Gilani summoned him to explain his remarks and a short time later, Mr Jatoi resigned
"We provided the army with uniforms and boots not so that they kill their own fellow countrymen, kill Nawab Sahib [Bugti] and Benazir Bhutto," he told a news conference in the city of Quetta.
Military might Former Pakistani Prime Minister Benazir Bhutto was assassinated in December 2007 as she was campaigning in Pakistan's presidential elections.Nawab Akbar Bugti was a tribal leader in the province of Baluchistan who was killed in a battle between government forces and tribal militants in August 2006.
Pakistan's military has carried out coups against the civilian government on three occasions - in 1958, 1977 and 1999 - and has governed the country for much of its 63-year history.
There has been speculation in the media that the Pakistani military would move against the civilian government, which was widely criticised for its handling of the recent floods.
However, most analysts believe a coup is unlikely at the moment.
During the same news conference, Mr Jatoi suggested that the benefits of corruption should be equally available to all.
"All groups — Sindhi, Pakhtun, Baloch, Seraiki and Punjabi - should get an equal share in corruption," he said.