The chief executive officer of enterprise software company SAP has resigned, after less than two years in the role. Leo Apotheker will be replaced by two co-CEOs, both current SAP executives.

“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,” said SAP founder and chairman Hasso Plattner.

Apotheker’s departure follows a difficult year for SAP. A dispute with customers regarding the pricing of its support services tarnished its reputation, while sales of its high-cost, on premise enterprise resource planning (ERP) software were hit especially hard by the economic downturn.

According to R “Ray” Wang, enteprise software analyst for the Altimeter Group, Apotheker was unlucky to hold the SAP reins during one of its most difficult years. “Leo was in the wrong time wrong place,” he wrote on his blog yesterday. “He entered a down market while in charge of a sinking ship.  Low morale among [SAP’s] engineering team, the issue with Enterprise Support and maintenance, and uncontrollable poor quarterly performance proved to be factors beyond his control.”

The newly appointed co-CEOs, Bill McDermott and Jim Hagemann Snabe, represent SAP’s sales division and its technology development division respectively. SAP has struggled to reconcile these two components in the past, and it remains to be seen whether this compromise will bridge the divide, or further entrench it.