The German company said late on Sunday it would return to split leadership with Bill McDermott, head of field organization and Jim Hagemann Snabe, head of product development, both already members of the SAP Executive Board, taking the helm.
The world's largest business-software company said the departure was by mutual consent and did not give a reason for the change at the top.
The new setup of the SAP Executive Board will allow SAP to better align product innovation with customer needs, the company said in a statement.
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 said.
In addition, SAP said, Vishal Sikka, Chief Technology Officer, has been appointed to the SAP Executive Board.
Apotheker was named as co-chief executive with Henning Kagermann in April 2008 and took over sole responsibility to lead the German company after Kagermann's retirement in July 2009.
Under Apotheker's reign SAP has had to announce job cuts of 3,000 staff, a first in the company's history.
Its sales were hit hard in September 2008 as companies reined in IT spending to combat the effects of the financial crisis.
But SAP staged a recovery on the back of cost cuts and managed to report a strong fourth quarter last month and Apotheker predicted a slow pickup.
In the past, SAP has relied on large, integrated software systems it has sold to many of the world's biggest companies.
But it has yet to adjust to the challenge of securing more smaller deals annually instead of selling one or two big expensive systems that are not in demand in an era of cost-cutting.
SAP also said that its co-founder and chairman, Hasso Plattner, had been asked to continue to play a strong role in advising the new leaders on technology and product development.
Plattner, who preceded Kagermann, has remained a powerful influence at the company in his role as chairman.
(Reporting by Nicola Leske in Frankfurt and James Mackenzie in Paris; Editing by Bernard Orr)