Beinish is set to retire on February 28, and be succeeded by Asher Dan Grunis.
Addressing the Supreme Court justices, the PM said Beinish served the court "wonderfully" during a difficult time, while withstanding criticism.
"I think that the court's independence is inherent and necessary, and in Israel the court has always been and will remain independent," he said, adding "any attempts to harm the independence of the courts will fall. I have shelved any proposal intended to harm or in any way undermine the independence of the court."
Beinish said during the ceremony she sensed Netanyahu was not always pleased with the court's rulings during her term, but supported the court nonetheless.
"For this I would like to express my gratitude and appreciation…Both professionally and personally I knew the prime minister would not abandon (the court)," she said.
"We are strong, very strong, but we also need the backing of the responsible authorities – and I felt that existed."
During Sunday's cabinet meeting, Netanyahu said he told incoming president Grunis that the government was "committed to bolstering the Supreme Court and uphold its independence as a cornerstone of Israeli democracy."
Moran Azoulay contributed to the report
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