The exit of Domenicali comes as Ferrari continues to flounder amid sub-par performances in the new era of the biggest technical changes in modern grand prix history.
In a statement Domenicali said he accepted full responsibility for the lacklustre position Ferrari finds itself in.
“Again, I take responsibility – as I always have – the situation we are experiencing,” Domenicali said.
“It is a choice taken with the desire to do something to give a jolt to our environment and for the sake of this group, which are closely linked.
“I sincerely thank all the men and women of the team, the drivers and partners for the wonderful relationship had in years.
“I wish you all that you can quickly return to the levels that Ferrari deserves.
Domenicali's successor, Mattiacci, is expected to take up the helm at the Maranello marque immediately.