The decision means Musharraf, 70, has been granted bail in three major cases against him, including one relating to the assassination of former Prime Minister Benazir Bhutto.
The decision in the case of rebel leader Nawab Akbar Bugti also increases the chances that the former dictator is released after nearly six months of house arrest, Dawn.com news reported.
Musharraf is a retired four-star general and a politician who seized power in a military coup in 1999 and later served as an elected civilian president from 2001-08.
His lawyer said the latest Supreme Court ruling means he is a "free man."
But for now he remains under heavy guard at his Islamabad villa where he has been under house arrest since April, ostensibly because of serious threats to his life, Dawn reported.
The Taliban have threatened to kill Musharraf for his close association with Washington's fight against terrorism after the Sept. 11, 2001, attacks in the United States.
Musharraf's latest bail concerns his fight against charges in the August 2006 death of Baluchistan tribal leader Bugti, 79.
He was a former Baluchistan province minister turned nationalist rebel who fought for provincial autonomy and a greater share of profits from Balochistan's natural resources.
But he was killed when a shell exploded in his mountain cave headquarters.
The Bugti case surrounds the circumstance in which the government raid on his cave took place and how the shell exploded.
The Supreme Court observed that no substantial evidence had been presented to involve Musharraf in the criminal conspiracy regarding Bugti's murder and granted him bail on $9,400.
Musharraf's spokesman Raza Bokhari said his client's fight will be a "long-run process."
"He will continue to fight these cases until his name is clear of these false, fabricated and fictitious charges," Bokhari said.
Despite the ruling, Musharraf also faces charges over the suspension and detention of more than 60 judges during emergency rule that he imposed in 2007.
Musharraf denies all charges against him, KarachiNews.net reported at the time.
Musharraf's troubles began in March when he returned to Pakistan from self-imposed four-year exile in London and Dubai.
He intended to run in May's national parliamentary election as head of his All Pakistan Muslim League Party.
But his arrests and detentions meant he failed to contest the election, which was won by Nawaz Sharif, 63 -- the man Musharraf toppled in the bloodless military coup in October 1999.
Other criminal charges against Musharraf stem from the death of former Prime Minister Benazir Bhutto in a gunfire and bomb attack while she was campaigning against him in 2007.
This week an anti-terrorism court in Rawalpindi granted a new trial request in the case of Bhutto.
But the court also said Musharraf will continue to be liable for prosecution, despite arguments that as president at the time he should have immunity.
The judges ordered the Federal Investigative Agency to present a list of witnesses at the next hearing, scheduled for Oct. 22.