Security forces also shot dead two other activists from Bhutto's Pakistan People's Party (PPP) party after a group attempted to force its way into an oilfield near Hyderabad.
Protests were held in the northwestern city of Peshawar, where more than 3,000 people chanted slogans against Musharraf.
Angry demonstrators also vandalised shops before being beaten back by police with batons and teargas, witnesses told AFP.
In Karachi, factories, stores and restaurants were set ablaze and burnt out cars littered the streets.
Another 2,000 people also rallied in the central city of Multan and similar smaller scale protests were held in Muzaffarabad in Pakistani-administered Kashmir and in Quetta.
Musharraf told his security chiefs Saturday to end the riots, saying those looting and plundering "must be dealt with firmly" in order to ensure the "safety and security" of the Pakistani people.
|Rioters burned and damaged scores of vehicles|
in Sindh province [AFP]
Estimates of the cost of the damage run into tens of millions of dollars.
Almost all of the deaths since Bhutto's killing have occurred in the southern province of Sindh, the PPP's power base.
Ghulam Mohtaram, Sindh's home secretary, told Reuters that rioters had burned or damaged 947 vehicles, 131 banks and 31 petrol stations on Friday alone.
Dozens of banks, vehicles and fast food outlets were also set on fire in Hyderabad on Friday.