Media reports last month suggested Red Bull's double champion Vettel had signed a pre-contract agreement with Ferrari, the sport's most successful and glamorous team, with a move likely in 2014.
Alonso, also a double world champion, has a contract with the Italian team until the end of 2016 and is very much the number one in the current line-up with under-performing Brazilian Felipe Massa.
Ferrari's official website (www.ferrari.com) published on Wednesday an interview of Domenicali and Formula One supremo Bernie Ecclestone by two German reporters who asked both men about Vettel.
Presented with a photo-montage of Vettel as he might look in Ferrari overalls, Domenicali smiled and said "in life one should never say never."
"I think they are both intelligent guys and they could easily co-exist together," he added when asked whether he felt Vettel could only move to Ferrari once Alonso was no longer at Maranello.
Alonso had a stormy time at McLaren when paired with Britain's Lewis Hamilton, who ended his extraordinary debut 2007 season level with the Spaniard on points but ahead in the standings as runner-up.
The Spaniard had eclipsed previous team mates and none of his subsequent partners have troubled him either. Massa has not been on the podium since 2010 and is out of contract at the end of the season.
Ecclestone, who is close to 24-year-old Vettel, said he would not advise him to move while still so young but recognised it was a possibility.
"Usually, a driver ends his career at Ferrari, therefore it could happen one day," said the 81-year-old Briton, who also played down the obstacles to an Alonso-Vettel pairing.
"That wouldn't be a problem: both are drivers who are always looking for a new challenge and to be in the same team would be a new and big challenge," he said.
"They would both think they can bear the other one, as they are sure of themselves and Stefano would do what was required to so that they were treated equally.
"It would be a case of doing what I did at Brabham in 1979 with Niki Lauda and Nelson Piquet. I told them, 'guys it's simple: whichever one of you is quickest is the team number one'," said Ecclestone.