A vehicle flush window system is provided for a vehicle door including a door window. The system includes a slider member, a guide structure, a glass run seal, and a capping carrier. The slider member is configured to be secured to an interior surface of the door window. The guiding structure is mountable on the vehicle door. The guiding structure includes a receiving bracket having a guide channel configured to slidingly receive the slider member. The glass run seal is interposed between the receiving bracket and the slider member in the guide channel. The capping carrier is configured to retain the seal, and mount a cover in flush relation to an exterior surface of the door window, when the interior surface of the door window is secured to the slider member and the slider member is slidingly received in the guide channel in a window closed position.