Mr Musharraf was restricted from leaving the country during the period that his bail was extended, reported the Associated Press.
Sixty nine-year-old Musharraf, who landed in Pakistan earlier this week ending four years of a self-imposed exile, had requested the Sindh High Court to extend bail; he was required to appear in person in court.
As he arrived in court this morning, escorted by security personnel in uniform, people, including groups of lawyers, shouted slogans against him. An angry protester, a lawyer named Tajammul Lodhi, threw a shoe at him which fell a few feet in front of Mr Musharraf.
Footage on TV showed the shoe flying through the air and landing in a group of people in front of Mr Musharraf. The man was later arrested by Pakistan Rangers.
Mr Musharraf had a shoe hurled at him in 2011 too, while he was addressing a gathering in Britain. He resigned as Pakistan president in 2008 and left Pakistan. He had been living in exile in Britain and the United Arab Emirates since.
He has returned to Pakistan to contest elections to be held in May this year. While in exile, he launched a political party, the All Pakistan Muslim League (APML), which he has said, will contest most seats.
In Pakistan, the former dictator faces not just the possibility of arrest on charges that inlude conspiracy to murder, but also death threats from the Taliban.
An anti-terrorism court had declared him a fugitive and in 2011 issued arrest warrants for him after he refused to cooperate with investigators probing Benazir Bhutto's December 2007 assassination. Last year, a warrant was also issued for his arrest over the killing of Baloch leader Akbar Bugti in a military operation in August 2006.
Mr Musharraf has denied all charges.