The Ramsay Street boss stands down from her post in December after four years in charge of the long-running show. She will then take on a new role within Neighbours' production company FremantleMedia Australia, which will include working on the business's international operations.
Bower, announcing her intention to depart Neighbours, told the Herald Sun: "It was a hard decision. I love Neighbours, it is a wonderful show and because of this I felt it was important that fresh eyes and brains take over to keep this Australian icon contemporary.
"Having said that, I'm really excited about the new role and thank FremantleMedia for this wonderful opportunity."
FremantleMedia's CEO Ian Hogg commented: "In her time with Neighbours, Susan has overseen the most significant and comprehensive change in the history of the production. Susan has revolutionised the creative and production processes of the show and, most importantly, the culture of the production unit.
"It is also during her tenure that Neighbours made a very successful transition from Ten to Eleven. Susan's passion and commitment have been inspiring, and I sincerely thank her for her dedication."
TV Tonight reports that former City Homicide boss Richard Jasek will be taking over as Neighbours' executive producer.
In a further change, Alan Hardy will also be joining the Neighbours team in the role of producer.
Hogg added: "Alan is a very hands-on producer with an incredibly strong script, casting and production sense. His early successes as script producer include The Sullivans, All The Rivers Run and The Henderson Kids.
"He has worked on a huge volume of Australian productions since and has most recently led the script team on Home and Away, City Homicide and Shortland Street. He will be a valuable addition to the Neighbours team."
> Read our July 2011 interview with Susan Bower
> Read more Neighbours news and spoilers