Nelson, who helped drive forward the move into multiplatform and digital operations at the BBC's creative arm, will leave his post at the end of 2010.
It is understood that Nelson's role will not be directly replaced, but instead BBC Archives director Roly Keating will take on his commissioning duties.
During his four-year stint at BBC Vision, Nelson has helped introduce a variety of digital initiatives, such as the recent EastEnders web-only spinoff E20 and Doctor Who: The Adventure Games.
"I've had 14 fantastic years in the BBC, leading the digital and on-demand transformation of first radio and now television," he told C21 Media.
"I've delivered everything and more that I set out to do in BBC Vision, including making Vision an integrated multi-platform operation. It now feels the right time to take the knowledge and expertise I've accumulated and develop it back in the commercial sector."
In a statement, BBC Vision director Jana Bennett said: "Simon has proved to be an advocate of digital media and also an architect of future commissioning and production structures within BBC Vision.
"Thanks to his work, programme makers now have the tools to create content across all platforms. This is an important and powerful legacy for the BBC and I am very grateful for his work on this as well as his contribution to the division as a member of the BBC Vision board."