Shahzad's body was found on Tuesday, about 150 kilometres south-east of Islamabad. Police said it bore marks of torture.
"The cause of death is torture and there are several signs of torture on his body and face," said Ashok Kumar, one of the doctors who carried out a post-mortem at Islamabad's Pakistan Institute of Medical Science.
Before his death, Shahzad told rights campaigners that he had been threatened by the Inter-Services Intelligence (ISI).
He vanished after leaving his home in Islamabad to appear on a television talk show, two days after writing an article about links between rogue elements of the navy and Al-Qaeda.
His relatives have demanded a full investigation but have not blamed anyone for his death.
Five years ago Shahzad was briefly kidnapped by the Taliban in Afghanistan and accused of being a spy.
US Secretary of State Hillary Clinton condemned his murder and said his "reporting on terrorism and intelligence issues in Pakistan brought to light the troubles extremism poses to Pakistan's stability".
Around 300 people, mostly relatives and journalists, attended the funeral prayers and Shahzad was buried in a local cemetery in the Seaview neighbourhood in his home town of Karachi.
The Pakistan Federal Union of Journalists announced two days of mourning and is organising protests across the country on Friday.
“Sources close to Shahzad said he had reported getting several warnings from the security agencies in the past in connection with his reporting,” says Paris-based media rights group, Reporters Without Borders. “This would tend to support the theory that he was kidnapped and killed in connection with his coverage of the attack on the naval base.”
The group says that 15 journalists have been killed since the start of 2010 in Pakistan.