CSU Chancellor Mildred García said Lee announced an agreement with pro-Palestinian student protesters without proper approval.
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In his original message, Lee endorsed student activism, protest and dissent.
RELATED: Sonoma State president on administrative leave after announcing agreement with protesters
"None of us should be on the sidelines when human beings are subject to mass killing and destruction," Lee had said Tuesday in announcing that an Advisory Council of Students for Justice in Palestine was being established at Sonoma State.
Lee later apologized, saying he marginalized some students in an attempt to find agreement with others.
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The CSU board has appointed Dr. Nathan Evans, the deputy vice chancellor for Academic and Student Affairs, as acting president.
"I thank President Lee for his years of service to the California State University-starting at California State University, Sacramento-and to higher education overall. I wish him and his family well," Chancellor García said in a statement.