Bugti led a tribal campaign to win political autonomy for resource-rich Balochistan, Pakistan's biggest province. He was killed in a military operation on the orders of then president and army chief Musharraf in the restive province in 2006.
Musharraf ordered the military crackdown in Balochistan in late 2005 after being targeted by a rocket attack while visiting the southwestern province.
72-year-old Musharraf, who also faces treason charges, was charged with the murder in January last year on the grounds he ordered Bugti's killing.
After the announcement of the decision by Judge Jan Muhammad Gohar, the lawyer representing Bugti's eldest son Jamil Bugti, Sohail Rajput, announced his decision to challenge the judgment of the court, the Dawn reported.
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"We are not satisfied with this judgement and we will challenge it," Rajput told reporters outside court.
In a separate application, Jamil had requested the court to summon the members of a parliamentary committee who had met Akbar Bugti following the violence in Dera Bugti in March 2005 in which dozens were killed.
Jamil had named Musharraf, former Prime Minister Shaukat Aziz, former Governor of Balochistan Owais Ahmed Ghani, ex-interior minister Sherpao and others for the murder.
Balochistan nationalists have accused Punjab, Pakistan's
most populous province, of exploiting their natural resources.
Musharraf never appeared in the court during the entire legal process which had been in progress since 2009. He was also absent when the charge-sheet was read out in the court.
He came to power in a bloodless coup in 1999, deposing then-prime minister Nawaz Sharif. Facing impeachment following elections in 2008, Musharraf resigned as president and went into self-imposed exile in Dubai.
The ex-army chief is facing a slew of court cases after returning from five years of self-exile in Dubai to contest the general elections in 2013 which he lost.
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.