Rabbi Eliezer Berland was convicted of sexually assaulting the women, kissing them against their will and rubbing himself against them, the ministry said in a statement.
Berland, 78, initially denied culpability but later accepted a plea bargain giving him the 18-month sentence.
He told the court today he "regrets his actions from the bottom of his heart", Israeli media reported.
"For such acts, the Bible would have pronounced the punishment of stoning," he supposedly added, promising to have no more contact with women.
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Many of the faithful remain convinced of his innocence despite his arrest at the end of a highly publicised manhunt.
The rabbi, who has a long white beard and wears a black outfit characteristic of ultra-Orthodox Jews, fled Israel in 2013 after several women laid charges of indecent assault against him.
He evaded capture in the United States, Switzerland, Morocco and Zimbabwe.
He was finally arrested in South Africa this year.
Berland rose to prominence in the 1980s for organising clandestine pilgrimages to the tomb of his movement's founder in Ukraine.
His Facebook page, followed by more than 17,000 people, asked his supporters to continue to back him.
Sara Markovitz, a lawyer for one of the complainants, denounced the agreement and criticised the absence of a full trial.
"The message to female victims of harassment is that filing a complaint is useless," she said.
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