Vettel secured his third successive title for Red Bull last season, becoming the youngest triple champion at 25, and has dismissed speculation that he already has a pre-contract to join Alonso at Ferrari in 2014.
Ferrari president Luca Di Montezemolo said last month that Vettel was a "potential Ferrari driver for the future" but he has also spoken against having "two roosters in the same hen house."
"Could Vettel and Alonso one day be part of a dream team? I think our president has already commented on this subject several times," Domenicali told reporters at a media event in the Italian Dolomite resort of Madonna Di Campiglio.
"A dream team is fantastic if it is correctly managed, but at the moment we are not looking at that, because we want to ensure the team is as well balanced as possible.
"You have to be very careful, not just in Formula One, but in sport in general, because sometimes putting together all the number ones can lead to more negatives than positives."
Ferrari have an unchanged line-up for 2013 after deciding to extend Brazilian Felipe Massa's contract for another year despite a poor first half of 2012.
Double champion Alonso ended last season as overall runner-up to Vettel, with the Spaniard scoring 278 points compared to Massa's 122.
Domenicali recognised he had come under pressure to hire a replacement but felt Massa's later form had vindicated the decision not to.
"I think the toughest part of Felipe's career is now behind him," said the Italian.
"I'm sure his problem was not linked to his contractual situation. Personally, there was a lot of pressure on me regarding possible changes, but in the interests of the team, I preferred to wait and today, I'm convinced that keeping Felipe in the Ferrari family was the right decision.
"His performance in the second half of the season contributed significantly to our second place in the constructors' classification: for the team that is a strong point and for Fernando, it provides further impetus to try even harder."(Reporting by Alan Baldwin, editing by Alison Wildey)