The high court struck down the decision of a lower court against a female former store employee whose wages were 35 percent lower than those of a male colleague.
That court had said the difference was legitimate and a result of contract negotiations not gender discrimination.
But the high court, in a decision by a panel of three judges published on Friday, found that "in certain cases it should be enough to prove the existence of a significant gap in wages for the employer to bear the burden" of meeting laws against gender discrimination.
Previously, it was up to a female employee to prove a claim of pay discrimination, making it difficult to have laws passed since the late 1980's outlawing pay inequality enforced.
"This is an historic ruling," said attorney Orna Lin, representing the Israeli woman behind the case. "Today an employer will think twice before paying two different employees different wages for doing the same work."
The judges pointed to Israeli government figures showing women earned an average of 66 percent of men's wages in 2010.
The average for OECD countries is about 84 percent, with Germany at 78 percent and the United States at 77 percent.
Ruth Halperin-Kaddari, a professor in women's affairs and a member of the United Nations Committee on Elimination of all forms of Discrimination Against Women (CEDAW) said the ruling put Israel more on a par with the West in its policy toward women.
"One of the major obstacles to rectifying wage inequities was that it was up to the women to prove the discrimination. Now this eases the way," Halperin-Kaddari said.