Michele Ferri is the brother of 51-year-old Andrea, a petrol station manager who was allegedly gunned down by two men including one young employee he treated like a son.
The death shocked the north-eastern town of Pesaro.
Michele Ferri wrote a letter to the Pope telling him of his inability to forgive the killers and was shocked when he picked up the telephone on Wednesday evening to hear: "Ciao Michele, it's Pope Francis."
At first Mr Ferri thought it was a joke but said he was overcome with emotion when he realised it was really Francis on the line from theVatican.
"He told me he cried when he read the letter I wrote to him," Mr Ferri said.
The Pope also asked to speak to Mr Ferri's mother to express his personal sympathy.
The telephone call is the latest in a series of spontaneous personal gestures by Pope Francis that have surprised Catholics around the world since he was elected Pope in March.
"I forgot to ask him if he wanted to visit us in Pesaro," Mr Ferri said.
Father Mario Amadeo, a town priest who knows the family well and conducted the funeral in June, said he did not know about the letter to the Pope until Mr Ferri's mother told him.
"It's a very beautiful gesture that indicates the kindness and greatness of this Pope," he said.
Pope Francis has adopted an informal approach since the night of his election when he greeted the crowds in St Peter's Square with a simple "Buona sera" or good evening. He has made daily contact with ordinary people a priority ever since and told a friend earlier this year he shunned the papal apartments because he did not want to be isolated.
Two men have been arrested and accused of firing seven shots at Mr Ferri through the windscreen of his car as he was driving home and fleeing with the key to his company safe.