An anti-terrorism court in the garrison city of Rawalpindi, next to Islamabad, put Musharraf on 14-day judicial remand over the death of the former prime minister, who was assassinated in a gun and bomb attack in 2007.
Musharraf returned from exile in March to stand in the May 11 general election, vowing to "save" the country from militancy and economic collapse but he was barred from running over charges dating back to his 1999-2008 rule.
He will now spend polling day in his Islamabad villa, which has been designated as a jail, making his chances of even voting now remote.
Musharraf's lawyer Ibrahim Satti told AFP that his client could request a postal vote but said a government-facilitated visit to a polling station would be unlikely "because of security concerns".
The retired general is already under house arrest for sacking judges when he imposed emergency rule in 2007 and did not appear in court in person.
"The court granted a 14-day judicial remand and ordered that Musharraf be kept in a judicial lock-up until May 14," prosecutor Chaudhry Zulfiqar told AFP.
The order was made to give investigators time to work on the case and the regular hearing is due to begin on May 3.
Musharraf is accused of conspiracy to murder two-time prime minister Bhutto, whose Pakistan People's Party (PPP) was elected into power in February 2008 on a wave of sympathy over her death.
Besides the sacking of judges, he faces a third legal case over the 2006 death of a Baluch rebel leader during a military operation and has been threatened with death by the Taliban.
His All Pakistan Muslim League party has complained that he has been confined to two rooms and stripped of his personal staff.
In the northwestern city of Peshawar, a court dismissed an appeal against his disqualification from standing for election in the district of Chitral and banned him for life from running for parliament, lawyers said.
Nobody has ever been convicted or jailed for Bhutto's assassination. Musharraf's government blamed the killing on Pakistani Taliban chief Baitullah Mehsud, who denied any involvement and was killed in a US drone attack in 2009.
But Bhutto's son, Bilawal Bhutto Zardari, who is PPP chairman, has accused Musharraf of her murder.
In 2010 a UN report said Bhutto's death could have been prevented and accused Musharraf's government of failing to give her adequate protection.