The police have arrested the former DIG from premises of the court.
Five Tehreek-i-Taliban Pakistan (TTP) suspects have been acquitted over lack of evidence.
The court also awarded 17 years imprisonment to former DIG Saud Aziz and SP Khurram Shehzad for abetting the crime.
By failing to bring its most prominent suspect, ex-president Musharraf, to justice, the anti-terrorism court in Rawalpindi set "a unsafe precedent", said Saroop Ijaz, a lawyer and researcher with Human Rights Watch in Pakistan. The prosecution also said the two police officers did not provide sufficient security to Bhutto after she received death threats from militants.
Musharraf was also among the list of accused, who is living in exile in Britain and the United Arab Emirates. The ruling Thursday ordered him arrested - should he return to the country - and his property in Pakistan seized for failing to show. He moved to Dubai in 2016 after a travel ban was lifted.
ATC judge Asghar Khan, had on Wednesday, reserved his verdict in the case after recording closing arguments by the prosecutor, Federal Investigation Agency (FIA), and counsels for the accused.
Saud Aziz, who was chief of the Rawalpindi police at the time, was accused of giving Shahzad permission to hose down the scene and of refusing to allow an autopsy of Bhutto's body to go ahead.
Eight different judges heard the case during this period who were changed due to different reasons.
In 2013, the chief prosecutor, Chaudhry Zulfiqar Ali, was shot dead by Islamist militants as he drove to a hearing.
Benazir Bhutto was killed in a gun-and-bomb attack after addressing a rally at Liaquat Bagh in Rawalpindi on December 27, 2007.
She was killed when she stood up and put her head out of a sunroof-style escape hatch in the bombproof vehicle.
Two suspects Ibadur Rahman and al-Qaida's No. 3 leader and financial and operational chief Mustafa Abu Yazid alias Sheikh Saeed Al-Masri are believed to have been killed in US drone strikes in Pakistan.
Educated at Oxford and Harvard, she became the first female prime minister of an Islamic country at the age of 35, after military dictator Zia ul-Haq died in a plane crash in 1988.
Musharraf's government blamed Bhutto's killing on Pakistani Taliban chief Baitullah Mehsud, who was killed in a USA drone attack in 2009.
Prior to her death, Bhutto said a sinister cabal of intelligence officers and presidential aides were plotting to kill her, and that Musharraf should be blamed if anything were to happen to her. PPP has always maintained that line. "So the mystery remains unsolved".
Mrs. Bhutto was a hugely important figure in Pakistani politics.
The verdict did not say who was the assassin of Bhutto. From exile, she maintained a firm grip on the Pakistan People's Party (PPP), sometimes to the resentment of allies who believed she ran it as a family fiefdom.