Judge Ilan Halbaga gave Esta, her 10-year-old son Qian and 5-year-old daughter Katherine 45 days to leave the country, "in order to provide them with the opportunity to settle their affairs before their departure, to say goodbye to friends and acquaintances, and to consult with experts who will recommend continued treatment for Qian in his own country."
Attorney Haya Mena, representing the family, said she would appeal the decision at Tel Aviv District Court.
The three were arrested Tuesday at their home in Ramat Gan after immigration officials broke down their door and have been detained at Ben-Gurion Airport since.
Halbaga said that the three can be released on NIS 15,000 bail, provided that Esta appears at the Population and Immigration Authority's offices every week.
Esta arrived in Israel 15 years ago to work as carer. Her visa expired in 2008, and she has been living illegally in Israel ever since.
Her two children were born after her visa expired and their father has since returned to the Philippines. Qian has just completed fifth grade in Ramat Gan and Katherine, who is not registered with the Population and Immigration Authority, attends a municipal kindergarten in the city.
In his ruling, Halbaga wrote: "There is no argument that the separation imposed on the children will first and foremost harm them, and I am prepared to accept that there will also be some harm to (Qian's) classmates.
"The natural difficulty involves moving from the country in which the children have been raised all their lives to a land that is foreign to them, but this difficulty exists in any case of minors born to migrant workers.
"In doing so, this consideration should be taken into account by the children of a father who has been residing in the Philippines for
He added: "As for the severity of Qian's suffering, there is no claim that he could not be treated in his country. I am prepared to accept that Qian suffers from asthma as claimed during the hearing, although no evidence has been presented, however this is unfortunately a common disease, and it is not alleged that medical treatment cannot be obtained in his own country."
The ruling criticized the considerable delay in submitting an application to settle the status of the family on humanitarian grounds, which their attorney said she intended to submit.
"Geraldine had to act within days and not linger for about a decade until restraining orders were issued. This is intolerable behavior," he said.
Nonetheless, Halbaga also wrote towards the end of his ruling that letters from Qian's friends and the statements by his friends' parents during the hearing were "heart-wrenching."
"It did not go unnoticed that the children must go to a country they have never visited and adapt to a living environment different to the lifestyles they have become accustomed to," he said.