The FIA announced last week a new 'winner takes all' system, in which the driver with the most wins would be champion, even ahead of a driver with more points.
The governing body also rejected a system proposed by the Formula One Teams' Association that would have increased the points advantage between the winner and the second-placed driver.
But, after complaints from the teams and drivers, the governing body admitted it was ready to defer the introduction of the new system if the teams were unhappy about it, and it now seems likely that the one used last year will stay on for 2009.
Domenicali said the situation was not good for F1, and admitted going back to the usual points system was not ideal either.
"It seems embarrassing to me what has happened in the last few days," Domenicali told the Gazzetta dello Sport newspaper on Monday.
"We wanted a bigger difference between the winner and the others, instead it stays like 2008. Oh well."
The Ferrari boss also said he is expecting the governing body to clarify the regulations regarding the rear diffusers, as F1 could be heading for another row at the Australian GP this weekend.
FIA president Max Mosley admitted a protest could not be ruled out after Sunday's race due to the diffusers used by Williams, Toyota and Brawn GP.
Domenicali is hoping the issue is resolved before there are protests launched.
"We are convinced that certain interpretations that have been applied do not correspond to the nature of the rules," he added.
"We expect the federation to clarify as soon as possible its position over the diffuser. If that extractor is illegal then it must not be used, while if it is legal it's up to the other teams, including us, to try to adapt as soon as possible, because performance is found in that area of the car."There needs to be a great sense of responsibility on everyone's part. I hope this issue can be resolved beforehand."