Court spokeswoman Ayelet Filo says the approval is for a trial period of a year.
Ultra-Orthodox practice forbids men from touching women, except for their wives. Men and women are separated in public. Recently on two bus lines serving their communities, women were instructed to sit in the back.
Human rights and women's groups objected, filing a suit with Israel's Supreme Court. The court ruled Thursday that the arrangement is legal as long as it is voluntary.
There have been several cases of women complaining that male passengers verbally abused or assaulted them when they refused to move back.