Lo Porto, 39, a native of the Sicilian city of Palermo, devoted his life "to serving others," Italy's Prime Minister Matteo Renzi said.
Lo Porto, known to his friends as Giancarlo, studied international relations in London with a focus on Japan and had worked for aid groups in Croatia, the Central African Republican, Haiti and Pakistan.
He returned to Pakistan on January 16th 2012 to lead reconstruction efforts for an area hit by an earthquake and flooding in 2010, as part of a project funded by the European Union. He was kidnapped three days later.
Lo Porto worked for a German NGO, Welthungerhilfe, and was abducted in a residence that housed foreign workers in the Pakistani town of Multan, according to Islamabad authorities. He was kidnapped along with a German colleague.
There was no direct "proof of life" after his kidnapping but there was indirect evidence when his German colleague in a 2012 video suggested he was not alone.
The German was later separated from his Italian colleague and released in October 2014, reportedly after a raid by German special forces.
Marc Gross, spokesman for Welthungerhilfe, told AFP that Lo Porto "knew the region well" having worked in Pakistan for an Italian aid group previously. In 2010, he had worked to help provide potable water in flooded areas.
"Lo Porto was well known and liked by his colleagues, and this is a very difficult time for us," Gross said.
"His family had not had contact with him for three years, and for them, this is particularly hard."
The Italian daily Corriere della Sera called Lo Porto a "a true volunteer" and "anything but an adventurer."
Obama revealed the deaths of Lo Porto and Warren Weinstein, an American aid worker killed alongside the Italian, on Thursday in an emotional apology.
The United States was not aware the two men were being held at a location that was targeted in a covert US counter-terrorism "operation" on the Afghanistan-Pakistan border against Al-Qaeda, Obama said.
Elaine Weinstein said that Al-Qaeda bore "ultimate responsibility" for her husband's death, and condemned their "cowardly" actions.
But she said her family was looking forward to seeing the results of a US government investigation into the strike.
She criticized the Pakistani government's attitude toward her husband's case and said assistance from the US government had been "inconsistent and disappointing" over the past three and a half years.