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In a short statement, the Detroit-based automaker said that "Rick Wagoner is stepping down as chairman and CEO, effective immediately."
Wagoner was asked to step down by the Obama administration as a precondition for the ongoing restructuring within the company.
Wagoner has been CEO since 2000 and has managed the company through some of its most difficult moments.
Over the last four years, GM has reported losses of 82 billion U.S. dollars and nearly ran out of money at the end of last year before the U.S. Treasury Department provided emergency loans.
GM has received 13.4 billion dollars in loans from the Treasury so far and said in February it needed up to 16.4 billion U.S. dollars in additional aid.
President Barack Obama said in an interview with the Columbia Broadcasting System on Sunday that embattled U.S. automakers had not done enough yet to become "lean, mean and competitive" under federal oversight.
Obama called for "sacrifices from all parties involved -- management, labor, shareholders, creditors, suppliers, dealers." He is expected to announce additional aid for GM and Chrysler LLC on Monday.
U.S. Treasury Secretary Timothy Geithner said Sunday the government is ready to help Chrysler LLC and GM restructure, but he declined to comment in detail on new steps expected to be announced by the White House Monday.