The Italian manager felt Michael Essien was harshly penalised for a handball in the Blues' box, stating his belief that the Ghanaian could not have avoided the contact
Michael Essien was penalised for blocking a shot with his arm but Di Matteo felt that the Ghanaian was hard done-by and did not have time to get out of the way of the effort from close range.
Sergio Aguero dispatched the resulting penalty and Samir Nasri added a late second goal to secure three points for Manchester City at the expense of the Blues, who took the lead through Gary Cahill.
"It was a bit harsh," Di Matteo told Sky Sports.
"It was a handball, for sure, but I don't think he [Essien] could have disappeared – he was very close to the ball.
Di Matteo felt that the equaliser gave City an injection of hope that they could find a winning goal, Chelsea had kept Roberto Mancini's side at bay up until that point and the 41-year-old praised his side's defensive display.
"I think we fought very hard and deserved a point at least," Di Matteo insisted.
"I think the penalty gave them a lift – we were defending very well at that point. It gave them just that little hope that they needed."
Fernando Torres did not add to the two goals he scored against Leicester City at the weekend before being replaced by Didier Drogba but Di Matteo was happy with the effort shown by the Spanish forward.
"I thought it was a terrific effort from him, and from the whole team too," Di Matteo said. "It's a good sign [that he did not want to be substituted]."
Defender Branislav Ivanovic was forced off with an injury in the first half, with Jose Bosingwa replacing the Serbian, but Di Matteo would not be drawn on the severity of the problem.
"It's his thigh muscle, but we'll have to assess him," Di Matteo added.