With the acquittal of the only men to have been charged with playing a direct role in Ms. Bhutto’s death, it was unclear if the long-running investigation and prosecution was drawing near a close. No one other than Mr. Musharraf is facing charges. The Pakistan Peoples Party said it would file an appeal of the ruling.
In freeing the five defendants, a judge in a special terrorism court, Muhammad Asghar, cited what he said was a lack of evidence. The defendants were Aitzaz Shah, Muhammad Rafaqat, Husnain Gul, Abdul Rashid and Sher Zaman.
The ruling came against a backdrop of intimidation and threats to the judiciary from militants, who have a history of attacking judges and lawyers and of intimidating witnesses. Judges in the Bhutto case changed frequently over the years, and hearings took place in the heavily guarded Adiala Jail on the outskirts of Rawalpindi.
The acquittal of the defendants set off wide disbelief, with some commentators calling the verdict “bizarre.” There was speculation in political circles that the judge might have been wary of militant reprisals. The Pakistani criminal prosecution system is also considered ineffectual.
In 2013, Chaudhry Zulfiqar Ali, a state prosecutor who was leading the efforts to prosecute Mr. Musharraf, was killed while he was on the way to court. Pakistani investigators later arrested three men — Abdullah Umar, Hammad Adil and Adnan Adil — in connection with his death.
On Thursday, Judge Asghar imposed 17-year prison terms and heavy fines on two senior police officers: Saud Aziz, who was the Rawalpindi police chief at the time of the assassination, and Khurram Shahzad, a former superintendent of police. They were accused of negligence in the Bhutto assassination.
Mr. Aziz has been criticized for having the crime scene hosed down within hours of her death. A United Nations investigation, published in 2010, found that a senior army officer had given the orders to Mr. Aziz to clean up the scene. The report also said that the failure of Pakistani authorities to effectively investigate the killing had been “deliberate” and that the investigation had been “severely hampered” by the country’s powerful intelligence agencies.
Just months after Ms. Bhutto’s assassination, Mr. Musharraf blamed Baitullah Mehsud, a former leader of Pakistani Taliban, for the killing. Investigators said Mr. Mehsud had provided the suicide bomber and arranged for the funds. In 2009, Mehsud was killed in an American drone strike
On Thursday, after the Bhutto defendants were cleared, senior officials of the Pakistan Peoples Party questioned the decision.
“The court verdict is a shock for me,” said Senator Rehman Malik, a former interior minister who was a close aide to Ms. Bhutto. He said: “The militants have been exonerated despite the hard evidence. The entire forensic record is against them, along with their own confessions.”
Mr. Malik also said Mr. Umar, one of the men accused of involvement in the prosecutor’s death in 2013, was a nephew of Khalid Shaikh Mohammed, the self-described architect of the Sept 11, 2001, attacks in the United States.
He said that three of the men accused in Ms. Bhutto’s assassination case were known Qaeda militants and that the Taliban had long been demanding their release.