Domenicali denies Ferrari gave team orders
The Maranello marque face the prospect of further punishment as the matter has been referred to the World Motor Sport Council.
Domenicali, though, has expressed his confidence "that the World Council will know how to evaluate the overall facts correctly".
The incident was sparked by a coded message to Massa on lap 47 that "Fernando is faster than you", which led to the Brazilian allowing by the double world champion two laps later.
Explaining the situation, and speaking before the fine was handed out, Domenicali said: "We gave information to Felipe about the situation.
"We have already seen in the past that certain situations did not provide the best result to the team (referring to the accident in Turkey between Red Bull drivers Mark Webber and Sebastian Vettel).
"So that was the information we gave and we left it to the driver to understand and take notice of it in order to make sure the team, in terms of results, gets the best.
"It is a shame in a situation like today, with a great performance, everyone is focused on this.
"Again, the most important thing is we always consider the team interest as the best for us at least.
"After three very, very heavy grands prix, we have recovered from a very difficult situation, so I am pleased for the team. That's very important."
Domenicali further dismissed suggestions he now has a number one and two driver within his team.
"I am very happy with Felipe's performance, no doubt," added Domenicali.
"Felipe will have his chance, and for the benefit of the team he will push for the championship, no doubt at all.
"There is no one and two."