Yes, you can do this using FrameworkElementFactory. Charles Petzold has a walkthrough of this in chapter 11 of "Applications = Code + Markup," but the basic idea is that you create a FrameworkElementFactory for the template root element (and further factories for any child elements), create a ControlTemplate, and set the VisualTree property of the ControlTemplate to the FrameworkElementFactory:
FrameworkElementFactory borderFactory = new FrameworkElementFactory(typeof(Border));
// set properties and create children of borderFactory
ControlTemplate template = new ControlTemplate();
template.VisualTree = borderFactory;
myButtonInstance.Template = template;