It was the Viola's third defeat on the bounce, which also saw Juan Manuel Vargas miss a spotkick.
Prandelli said: "Unfortunately we asked for sacrifices from our players. Today we picked up three injuries in the opening 35 minutes and missed a penalty.
"We apologise to everyone, but it is a situation that must force us to reflect on the future. We are very disappointed."
Prandelli turned to tell some supporters to calm down behind his bench after they started jeering.
"In these five years the fans have shown great maturity. I am convinced that within a few days we will shake off this disappointment and focus on the future, more united and stronger than ever."