Musharraf was driven to the court in Rawalpindi, the headquarters of the army he once led, from his plush villa on the edge of Islamabad where he is serving a two-week arrest order for other charges dating back to his 1999-2008 rule.
Musharraf is accused of conspiracy to murder Bhutto, who died in a gun and suicide attack in December 2007. It is one of three cases he is fighting in the courts since returning home last month after four years in self-imposed exile.
His arrest and disqualification from contesting elections on May 11 have been a humiliating blow for the former ruler of nuclear-armed Pakistan, previously a key ally of US president George W. Bush in the war on terror.
Despite a heavy police and paramilitary presence, scuffles broke out between lawyers and Musharraf supporters, who threw stones and beat each other with sticks outside the court building, an AFP reporter said. About 150 lawyers shouted: "Dog, dog, Musharraf dog!" while two dozen supporters chanted "Long live Musharraf!"
Musharraf spent around 15 minutes in court and then another 15 minutes with his lawyer, before being driven back to his home.
Nobody has been convicted or jailed for Bhutto's assassination on December 27, 2007, in Rawalpindi, despite a long-running court case.
In November 2011, the court indicted two police officers and five alleged Taliban militants over her assassination.
In August 2010, it ordered the confiscation of Musharraf's property and the freezing of his bank accounts in Pakistan over his failure, while in exile, to appear to answer questions related to her death.
Safdar told AFP that Musharraf's team asked the court to rescind those orders, given that he was now prepared to appear in court, complained that lawyers had been barred from meeting him and ordered police to investigate.
The court adjourned until May 3.
Musharraf's government blamed Bhutto's killing on Pakistani Taliban chief Baitullah Mehsud, who denied any involvement and who was killed in a US drone attack in August 2009.
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.
Bhutto's son, Bilawal Bhutto Zardari, who is chairman of the outgoing Pakistan People's Party, has accused Musharraf of her murder.
On Monday, Pakistan's caretaker government refused to put Musharraf on a separate trial for treason, saying it was beyond its mandate and up to the incoming government, which will be elected on May 11.