Granata was a victim of the Virginia Tech massacre on April 16, 2007. Upon hearing a commotion from his office on the third floor of Norris Hall, the professor brought 20 students from a nearby classroom into his office, where the door could be locked. He and another professor, Wally Grant, then went downstairs to investigate the situation. They were both shot by Seung-Hui Cho; Grant was wounded and survived, but Granata died from his injuries. He was 45 years old. None of the students locked in Granata's office was injured.

One of Granata's fellow Virginia Tech engineering professors, Dr. Liviu Librescu, was also killed in the shootings. The Engineering Science and Mechanics Department Head, Dr. Ishwar K. Puri, remembered Granata and Librescu in a statement as "world-class" researchers. Dr. Puri stated about Granata, “The use of his research by other scholars worldwide had put him on a trajectory to become a notable star in these fields.”

Memorial services were held in Blacksburg and a funeral mass at Christ the King Church in Toledo, Ohio, where his parents, Joseph and Mildred, and siblings live, was later held.