His kidnapping in Islamabad on May 29 was followed by the discovery and identification of his tortured corpse in an irrigation canal 170 kilometers from the Pakistani capital.
The death of Shahzad, who was buried on June 1 in Pakistan's southern seaport city of Karachi, has prompted journalists to protest across Pakistan. Moreover, it has even resulted in a government order allowing journalists to carry firearms to protect themselves.
Numerous questions are being asked; about the life and work of Shahzad, and why someone would want him killed.
Shahzad was known for his investigative reports about terrorism and security issues. He was the Pakistan bureau chief for the Hong Kong-based "Asia Times Online" and also wrote for Adnkronos International -- an Italian news agency.
Killing Raises Awkward Questions
In the first part of a two-part investigative report on May 27, Shahzad broke a story on alleged secret negotiations between the Pakistani navy and Al-Qaeda whose failure, he concluded, led to the attack on a naval base in Karachi on May 22.
Two Pakistani naval surveillance planes were destroyed in that 15-hour battle, in which 10 officers and soldiers were killed.
"The naval intelligence had traced an uneasy grouping inside the naval bases," he said. "And the lower cadres of the navy were discovered to have planned to attack foreigners while they visited naval installations."
Shahzad is among a growing numbers of Pakistani journalists killed in the line of duty.
The lives of 15 journalists have been lost in as many months, making Pakistan the world's most dangerous media environment.
These journalists died as a result of insurgent violence and targeted assassinations.
Despite government promises, so far none of the killings has been resolved, and the names of the deceased are forgotten once they drop out of the news cycle.
Recipient Of Countless Threats
Islamabad-based correspondent Tahir Ali knew Shahzad for years. He remembers him as a kind friend who fearlessly pursued news.
Ali says that Shahzad often traveled to remote regions of Pakistan and Afghanistan to research complicated stories. He was briefly held by the Afghan Taliban in the southern Helmand province in 2006.
According to Ali, Shahzad received countless threats over the years, most of which were attributed to Pakistani intelligence agencies who warned him to stay away from controversial issues.
"Last year he broke a story about the release of [Afghan] Taliban leader Mullah [Abdul Ghani] Baradar from Pakistani custody," says Ali.
"After that, the [intelligence] agencies threatened him. Although these were not direct threats, he was once told, 'We have arrested a militant who has a list of targets. We will do you a favor if we find your name on those lists.' This was an indirect threat to him, indicating that [they] can do anything to you."
Shahzad had informed Human Rights Watch that he was under threat from Pakistan's military intelligence agency.
Intelligence Agency Denies Involvement
"We can't say for sure who has killed Saleem Shahzad," Ali Dayan Hasan, senior South Asia researcher for Human Rights Watch told the Reuters news agency. "But what we can say for sure is that Saleem Shahzad was under serious threat from the ISI, and Human Rights Watch has every reason to believe that that threat was credible."
The Pakistani intelligence agency refutes such allegations. "[The] ISI offers its deepest and heartfelt condolence to the bereaved family and assures them that it will leave no stone unturned in helping to bring the perpetrators of this heinous crime to justice," an unnamed official told the government-run Associated Press of Pakistan news agency.
Pakistani Prime Minister Yousaf Raza Gilani has ordered an inquiry into his kidnapping and killing.
Pakistani journalists are not satisfied with official pronouncements. Speaking to Reuters after his funeral, journalist Mohammad Hanif said that only an impartial investigation would clear security agencies of any suspicion.
"All circumstantial evidence points toward our own intelligence agencies, that they are somehow complicit in it," he says. "Even if they are not, it is their responsibility to trace Saleem Shahzad's killers,"
Mohammad Anwer, a journalist and close friend of Shahzad, says that his murder is a signal that warns others to stop covering sensitive issues.
"By killing him, a shut up message has been sent to journalists that if you do this honest journalism, we will make an example of you like this."
A Humble Man Who Supported His Colleagues
Shahzad, 41, left behind three children. Ali says that Shahzad took great pleasure in helping fellow journalists. Months before his death, he established the website Asia Despatch (http://www.asiadespatch.com) to support unemployed journalists. He paid for the website but distributed its revenues to colleagues in need.
"Saleem Shahzad was a very good person who was very simple. I never saw a hint of hubris in him. He would make an extra effort to reconcile after falling back with friends. When any of his friends would lose a job, Saleem Shahzad would support him until he would find another job."
Shahzad began his career as a city correspondent for an evening paper in Karachi. After 9/11, he wrote about Al-Qaeda and the Taliban. Shortly before his death he published his first book "Inside Al-Qaeda and the Taliban: Beyond Bin Laden and 9/11."
Arman Sabir, an Islamabad-based producer for the BBC's Urdu Service, first met Shahzad in the late 1990s when both men worked for a private news agency in Karachi. He maintains that Shahzad's energetic reporting was mission oriented.
"He wanted to do something that nobody else had done," Sabir says. "And he didn't care for his life in his relentless pursuit of news. He was always obsessed in looking for news -- particular issues that were difficult for other reporters to investigate because of dangers. He was not afraid of playing with fire."
Sabir remembers the smiling face of his departed friend. "He was polite and never offended by anything, but always backed his assertions with strong arguments."
RFE/RL Radio Mashaal correspondent Gul Ayaz contributed to this report