Massa was given an instruction from the pit wall in the early stages of the Suzuka race on Sunday to give up his position to Fernando Alonso.
The Brazilian chose to keep on racing and, in the end, Alonso had to work hard to overtake him.
Domenicali said that Massa's defiance was not a concern, and he fully understood the motivation of his driver as he fights to secure a race seat for 2014.
"Felipe is trying to be as quick as possible, and I can understand his feeling," said Domenicali.
"But of course he will find the team totally supporting him until the end of the season, no problem.
"At the end of the day Fernando overtook him on track."
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