A team of Balochistan Police arrested the former military ruler and grilled him for nearly four hours at his farmhouse on the outskirts of Islamabad, which was declared a "sub-jail" by authorities.
The five-member police team confirmed to reporters outside the sprawling farmhouse that Musharraf had been arrested over the killing of Bugti.
Musharraf, 69, was the army chief when the operation against Bugti was ordered.
Shortly after the judge issued the order, the police team went to Musharraf's farmhouse to question him.
More From This Section
Musharraf is facing charges over the death of Bugti.
A court in Balochistan had issued a warrant for his arrest in 2011.
Since his return to Pakistan in March, Musharraf has also been arrested for detaining more than 60 judges during the 2007 emergency and over the assassination of former premier Benazir Bhutto.
In a related development, Aftab Ahmed Khan Sherpao, who was Interior Minister in Musharraf's regime, appeared in an anti-terrorism court in Quetta for the hearing of a case over Bugti's killing.