"Resignations in Italy are rare," said Montezemolo, who appointed Ferrari North America chief Marco Mattiacci - an unknown within the F1 community - as Domenicali's successor.
"Despite having won several world titles in 23 years, Domenicali had the strength to step down because of missed results," Montezemolo is quoted by La Stampa.
Criticism of Mattiacci's appointment, however, has been swift.
Patrick Tambay, a former Ferrari driver, told France's RMC that Domenicali is obviously a "scapegoat".
Some corners of the international media accused Ferrari of panic, and kneejerk reactions after only the first three grands prix in 2014.
Italy's authoritative La Gazzetta dello Sport confirmed that Mattiacci's appointment has been met with "scepticism".
"He needs to overcome it and assert himself in his new role," the sports daily advised.
La Gazzetta also pointed out 44-year-old Mattiacci's inexperience, saying that while he is a marketing specialist, his only motor racing experience is in Grand-Am sports cars.
Montezemolo insisted: "I have decided to focus on a young manager that I believe in a lot.
"I have heard and read many misplaced comments, for example that Mattiacci is not an engineer. But we are all Ferrari engineers.
"I wanted to focus on someone who is part of the Ferrari family, because we are full of people with many qualities and skills," he said.
Montezemolo added that Mattiacci's appointment was done "in full agreement" with Fiat chief Sergio Marchionne.
Mattiacci will be introduced to the F1 media on Friday in Shanghai.
"Now I am expecting a big reaction," Montezemolo, who will not be in China, concluded. "We will get back to winning and not allow the new rules to ruin the sport. For us, formula one is life."