The Nerazzurri were leading 3-1 with less than 30 minutes to play, but the controversial decision to award the visitors a spot kick sparked a comeback that saw the hosts lose to a 12-minute German Denis hat-trick.
"Doubtful? Let’s just say non-existent," Stramaccioni told Sky Italia when asked about the penalty.
"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 it upon himself to see something that did not happen. He took the responsibility for an event that did not exist.
"We thought it was Ranocchia’s challenge, but it turns out it was a [Walter] Samuel handball, when it didn't hit his hand. It’s incredible."
The 37-year-old also admitted that his side's Champions League aspirations have been scuppered by the loss."I don’t think we can still aim for third place. We have lost an ugly game and will try to play every remaining match at our best in Serie A and the Coppa Italia."