The German software maker confirmed in a statement he had left by mutual consent after it decided not to renew his contract that expired in December 2010.
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As a result, the board has named Bill McDermott, currently SAP head of field organisations and Jim Hagermann Snabe, who is in charge of product development as joint CEOs.
"The new set-up of the SAP executive board will allow SAP to better align product innovation with customer needs," said Hasso Plattner, co-founder and chairman of SAP.
Twenty year SAP veteran Apotheker took the helm in May - following 13 months as joint CEO with Henning Kagermann - but was unable to prevent the firm posting its first drop in sales since 2003.
Revenues for calendar year 2009 went down 3% to €8.2bn (£7.17bn), as profits dipped 4% to €1.8bn (£1.57bn).
Not only has the company wrestled with the acute slowdown in enterprise software roll outs during the recession, but it has come under fire from rival Oracle which has also acquired Sun and plans to take greater control of the Java platform.