Alonso's lead has steadily been eroded since his victory in Germany in July.
The Spaniard's advantage over Sebastian Vettel was 44 points when he left Hockenheim after his third win of the season but it is now just four points after his first-lap retirement in Sunday's Japanese Grand Prix.
Red Bull's Vettel took pole position, fastest lap and race victory to make the most of Alonso's retirement.
And with Ferrari having been consistently outpaced by McLaren and Red Bull over recent races, particularly in qualifying, it is now hard to see Alonso retaining his lead.
Ferrari's challenge has not been helped by a problem with their wind tunnel, which has seen updates fail to deliver the expected improvements on track. Not an ideal situation to be in when a big step forward in performance is required.
To that end Domenicali left Suzuka a few hours after the completion of Sunday's race to return to his desk at the Ferrari factory in Maranello, before again heading east for this weekend's Korean Grand Prix.
But he has urged his team to remain focused and confident over the final five races of an unpredictable season.
He said: "We have to stay calm, we know every race is different, we know what has happened to us in Japan can happen to the others.
"Right now we are not very happy and some other people are very happy, but it can be different very soon.
"At this stage of the season, the important thing is to stay rational and not fall into letting the others put us under more pressure and the team understand this is crucial.
"It is an important moment of the season, we have the opportunity to react next Sunday in Korea, so we will keep our heads up and we need to be very cool.
"It is a very critical moment to keep everyone focused and react in a proper way and not in a peak of emotion and do something beneficial for our competitors."
Domenicali has vowed the team will be looking to bring updates for the F2012 to all the remaining races to try to ensure Alonso wins his first title with the team he joined in 2010.
"When I hear people say we have not developed the car for many races, it is not true," he said.
"The reality is the level of competition is very high. We need to improve the qualifying pace as that is not the level we can be at.
"For sure we will try to bring steps, the reality will be seen on track but the target has to be that every race there is something new that can be incorporated because we need to maximise performance at every track.
"Having scored zero points the situation is we need to finish ahead of Vettel one way or another. If they have problems we have to be sure we score more points."