Rumours of Dempsey's departure have been swirling recently, and the actor spoke about exiting the series last November.
He told the Portland Press Herald he would be leaving the show very soon.
Rhimes says she "never imagined" saying goodbye to Derek Shepherd.
"Patrick Dempsey's performance shaped Derek in a way that I know we both hope became a meaningful example - happy, sad, romantic, painful and always true - of what young women should demand from modern love," she said in a statement published on People.com.
Dempsey is not the first regular to exit Greys. Katherine Heigl, Isaiah Washington, T.R. Knight, Eric Dane, Chyler Leigh, and most recently, Sandra Oh, also departed the series.
Patrick Dempsey stars as Derek Shepherd on Grey's Anatomy.
• Grey's Anatomy airs in New Zealand on Tuesdays at 9:45pm on TV2.