Stramaccioni's men had built a 3-1 lead at the San Siro when the visitors were awarded a controversial penalty.
German Denis converted and went on to complete a quick hat-trick as Atalanta came back to record a memorable away victory.
Stramaccioni has insisted that Gervasoni's performance was well below par and has admitted that his position as Inter coach remains perilous as a result.
When asked about the penalty award, he said: "Doubtful? Let's just say non-existent. We asked for five minutes what on earth it was for, but the referee took on a huge responsibility with this decision.
"The Atalanta players were going towards the corner, because they didn't see anything either. I don't think Gervasoni made a mistake. I think he took the responsibility upon himself by seeing something that did not happen. We thought it was for Andrea Ranocchia's challenge, but it turns out it was a Walter Samuel handball offence, when it didn't hit his hand. It's incredible.
"We have so many problems and even lost Antonio Cassano to injury today. It's true we have problems and some blame, but we are not so strong as to fight back against all these refereeing errors. I am new to Serie A, I came out of nowhere and they might send me back there at the end of the season, but I find it impossible that the referee could award a penalty like that."
Inter currently sit fifth in Serie A, eight points off city rivals AC Milan in the final Champions League place.