The Viola never were able to get a grip on the game from the moment Ferreira Pinto struck in the sixth minute for the hosts.
"This was our third game in a week and we used up so much energy against Inter," said Prandelli.
"We had players who needed to recover and weren't aggressive enough today. When we take the pressure down, then we allow our opponents too much time on the ball, even if we had chances too.
"Stevan Jovetic failed a fitness test and he even tried again at half-time, but he had physical problems and could not play," explained the Coach.
"Now we have to react and have the mental strength to play with the right spirit in these final four games.
"At the end of the season we will analyse the squad and consider where we can improve. I expect more organisation and discipline."