The Italian squad decided to break one of the seals in Massa's gearbox just before the race so the Brazilian would get a five-place penalty that would put Alonso in seventh position, and more importantly, on the clean side of the grid for the start.
Drivers had already expressed their concerns about the disadvantage of starting from the dirty side.
Alonso had a very good start and moved from seventh to fourth on the opening lap of the race. He finished in third position and kept his championship hopes alive going into the season finale.
Massa said after finishing in fourth that he understood the decision, but that he was not happy about it.
Domenicali insisted after the race that it was the right call and he is convinced any other team would have done the same in his situation.
"Yes, otherwise we wouldn't have done it," Domenicali said. "I prefer to be totally transparent, because with something like that you can easily simulate something if you want. But I felt it was more correct to say the truth. This is our style, my style.
"It is something that is our responsibility to do and retrospectively we knew that the difference in grip level on the two sides was very high. And we knew that if we were thinking of trying to be in the fight in Brazil it was very important to have the first car in front in the first couple of laps, otherwise the race would have been almost finished.
"At the end of the day, retrospectively, I think that was the right thing to do. When you work for the Ferrari team you know that the team is the centre of the decisions and the drivers respect it. I have to thank Felipe for that."
The Italian reiterated his belief that Massa had understood Ferrari's reasoning.
"I think he understood. I explained to him the decision. I have to say that if another team principal is saying that we didn't make the right choice he's lying to you," he said.
Domenicali admitted Ferrari had thought about the possibility of Red Bull doing the same with Sebastian Vettel's team-mate Mark Webber in order to put Alonso on the dirty side of the track again.
The team boss said that was the reason why he waited until the last minute to make the call.
"Yes, that's why we waited until the last moment to do it. It's part of the strategic things you have to decide. That's part of the game," Domenicali said.
He admitted, however, that Ferrari did not think about the drivers who had qualified behind Massa and that were affected by the penalty.
"To be honest, no. I say the truth. If I said it the other way around you wouldn't believe me, so I say no."
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