Bugti, who led a tribal campaign to win political autonomy for resource-rich Balochistan and a greater share of profits from the province's natural resources, was killed in a military operation on the orders of the then president and army chief Musharraf in the restive province on August 26, 2006.
Musharraf had ordered the crackdown in Balochistan in late 2005 after being targeted by a rocket attack while visiting the southwestern province.
The application had been filed by the Baloch nationalist leader's son, Jamil Akbar Bugti, in 2016, challenging the verdict of an Anti-Terrorist Court (ATC) in Quetta that acquitted the 74-year-old former military dictator and others in the case.
A divisional bench of the Balochistan High Court (BHC), comprising justice Jamal Mandokhail and Justice Nazeer Ahmed Langove, dismissed the application challenging the acquittal and maintained the judgement of the ATC, Dawn news reported.
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"We will challenge the BHC dismissal of our application in the Supreme Court," he said.
The death of the Baloch chieftain had sparked angry protests in parts of the country.
Jamil Bugti had named Musharraf, former Prime Minister Shaukat Aziz, former interior minister Aftab Ahmed Khan Sherpao, former governor Balochistan Owais Ahmed Ghani and others in his father's case.
Musharraf came to power in a bloodless coup in 1999, deposing the then-prime minister Nawaz Sharif. Facing impeachment following elections in 2008, Musharraf resigned as president and went into self-imposed exile in Dubai.
He is also facing trial in high treason case for abrogating the constitution in 2007 and illegal detention of judges same year.
Musharraf has also been charged in connection with the 2007 assassination of prime minister Benazir Bhutto and the killing of a radical cleric in Islamabad in a military crackdown.
He again left Pakistan in March last year after the government lifted a travel ban on him.