In a statement the company said it has replaced Apotheker with two Co-CEOs: Bill McDermott (head of field organisation) and Jim Hagemann Snabe (head of product development).
No explanation for the Apotheker's sudden departure was given by SAP but a media and analyst briefing is expected soon.
"The new setup of the SAP Executive Board will allow SAP to better align product innovation with customer needs. The new leadership team will continue to drive forward SAP's strategy and focus on profitable growth, and will deliver its innovations in 2010 to expand SAP's leadership of the business software market," SAP co-founder Hasso Plattner said in a statement.
CTO Vishal Sikka has also been appointed to the executive board as a result of the developments.
The news comes shortly after SAP reported a global 9 per cent year-on-year fall in revenue for the fourth quarter of 2009, with net income dropping 12 per cent from its record level a year earlier.
However, domestically strong investment by the retail, financial services, utilities and public sectors lead to a strong revenue growth for SAP Australia and New Zealand in 2009.
The software giant recorded overall year on year revenue growth of 11.3 per cent for the year to 31 December 2009.
Software and software related services revenue grew 14.4 per cent year on year and business user revenue from the SAP BusinessObjects line-of-business grew 126 per cent year on year.