The 37-year-old coach accepted that his side were deservedly beaten by the Partenopei and says investigations are underway in a bid to solve the club's injury crisis
An Edinson Cavani hat-trick blew the Nerazzurri away, with a Ricardo Alvarez penalty briefly bringing the visitors level at 1-1 midway through the first half.
The 37-year-old coach believes his side produced a strong performance in spite of a depleted strike force, but did not detract from the performance of Walter Mazzarri's men.
"Tonight I can only compliment Napoli, they played a great match and deserved the win. Cavani was amazing but we were both at the same level until 3-1," he told reporters.
"After we equalised we were unlucky, we did better in the second half before Cavani's third goal. Despite our absences, we put on a good show against Napoli who deserve second place."
The Nerazzurri earned a rare penalty in the first-half when Alvarez was brought down in the area by Juan Zuniga, though Stramaccioni believes the defender was lucky not to have faced further punishment.
"Was it a foul by Zuniga? The penalty went in our favour but he got away without punishment, while prior to the penalty awarded to Napoli, Jonathan was shown a yellow card," he added.
"My protest was to demand an explanation from the referee. I asked why Zuniga had not been sanctioned in this regard."
Stramaccioni also confirmed Inter have launched an investigation into potential causes behind their growing injury-list after captain Javier Zanetti last week became the latest player to be consigned to a long-term absence.
"Reasons for all the injuries? We are investigating this issue, though it must be said that we have suffered many muscle injuries. With the joints there is little we can do," the trainer said.
"Now we must think about finishing the season well. We came to the San Paolo to play an open game."