Rose Fostanes, the only foreign contestant on the show, moved to Israel six years ago, obtaining a visa to work as a carer for the sick and elderly.
Her success, which saw her winning last week's final with a soaring rendition of Frank Sinatra's "My Way," sparked celebrations across the Philippines and praise from its President Benigno Aquino.
But Israeli immigration officials said her visa did not allow her to work professionally as a singer.
The minister "ordered the population and immigration authority to grant Rose Fostanes permission to work as a singer in Israel," it said.
"Minister Saar decided to agree to her request and allow her a work permit as an artist," it said, noting such permission was subject to the agreement of the family she had been working for.
Fostanes has been likened by fans to Susan Boyle, the middle-aged Scottish singer whose humble looks and shy demeanour belied a scintillating voice that captivated millions on the television talent show "Britain's Got Talent" in 2009.
