Domenicali stepped down on Monday, after a torrid start to the season, culminating most recently in the team's drivers trailing in ninth and 10th in Bahrain two weeks ago.
"Stefano is a great man, first of all, and I am a close friend of his -- that is no secret," said Alonso in a press conference ahead of Sunday's Chinese Grand Prix.
"We still have a close relationship, we have been talking throughout the week, and that will continue because we have known each other for many years," added the two-time world champion.
Alonso added that he did not even know if Mattiacci would turn up in Shanghai for the weekend.
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However, team sources indicated to AFP that Mattiacci was flying in on Thursday night and is due to meet his team for the first time on Friday.
Nevertheless Alonso stressed that it was paramount to support the new boss and move forward. "We need to give him time and get the team behind him," he said.