- 12 updates
Chaudhry Zulfikar was shot at least 13 times as he drove to court in the capital Islamabad.
He then lost control of his car, which hit a woman passer-by and killed her, police said.
Mr Zulfikar was also prosecuting militants linked to the 2008 terror attack in the Indian city of Mumbai.
Although the motive for the killing was unclear, the prosecutor's involvement in the two high-profile cases is likely to be scrutinised closely.
Chaudhry Zulfikar, the lead prosecutor, investigating the 2007 assassination of former Pakistani Prime Minister Benazir Bhutto, has been shot dead while leaving his home.
Mr Zulfikar was gunned down as he drove to court in the capital Islamabad, a female passerby was also killed during the attack, police said.
Government prosecutors have accused Pervez Musharraf of being involved in Benazir Bhutto's murder and not providing enough security to the former Pakistan prime minister.
He has denied the allegations.
Police officer Mohammed Ishaq said killed prosecutor Chaudhry Zulfikar was also involved in a case related to the 2008 terrorist attack on the Indian city of Mumbai that killed 166 people.
The attack was blamed on a Pakistan-based militant group.
The lead prosecutor in the case involving Pakistan's former military ruler Pervez Musharraf has been shot dead, according to police, the Associated Press has reported.
Police officer Mohammed Ishaq says Chaudhry Zulfikar was gunned down this morning in the capital Islamabad as he was driving to court.
Mr Ishaq said Zulfikar was investigating the assassination of former Prime Minister Benazir Bhutto in a gun and suicide attack in 2007.
A Pakistani judge has ordered the former military ruler Pervez Musharraf be held in custody for two more weeks, until his next court hearing.
The hearing relates to Musharraf's 2007 decision to sack and detain several judges.
The development is the latest act in the drama surrounding Musharraf that erupted earlier this week and climaxed with his arrest on Friday after a speedy escape from another court hearing.
The former general, who seized power in a coup and ruled Pakistan for nearly a decade, has seen his fortunes plummet since he returned in March after four years in self-imposed exile.
The judge's ruling said that Musharraf would be given judicial remand, which means that he would be held in jail until the next hearing on May 4.
Pakistani police have arrested former President Pervez Musharraf, Musharraf's spokesman has told Reuters.
Pervez Musharraf's lawyer, Qamar Afzal, said his client had voluntarily presented himself at a Pakistan court.
Mr Afzal said he had asked the court to order police to place Musharraf under house arrest at his residence rather than put him in jail.
Another lawyer for Mr Musharraf told Reuters his legal team plans to appeal the arrest order later today.
The former army chief, who ruled Pakistan from 1999-2008, returned to Pakistan last month from nearly four years of self-imposed exile in the hope of running in next month's general elections.
But his bid to run for office has been rejected by election officials and he has instead found himself battling a host of legal challenges relating to his years in power.
Former Pakistan president Pervez Musharraf has been allowed to return home after appearing in an Islamabad court following his arrest.
Mr Musharraf was escorted by uniformed officers to an Islamabad court, a day after a judge issued an arrest order for the former army chief.
Police in Pakistan said they have arrested the country's former president Pervez Musharraf, who went on the run after his bail was revoked in his treason case.
It is understood the ex-military ruler was arrested at his home in Islamabad and has now been presented again before a court.
Mr Musharraf fled the courtroom yesterday after his bail was cancelled in a case related to the dismissal of judges during his time in office.
Former Pakistani military ruler Pervez Musharraf and his security team pushed past police and sped away from a court after his bail was revoked in a case where he is accused of treason.
The Islamabad High Court ordered his arrest after refusing to extend his bail, the Associated Press cited a police officer as saying.
Local television broadcast footage of Musharraf jumping into a black SUV and fleeing as one of his bodyguards hung to the side of the vehicle.
Prosecution lawyers chanted, "Look who is running away. Musharraf is running away", as the SUV left the scene.