A windowpane is specifically a single sheet of glass set into a window frame. Pane is a broader term that can describe any flat section of a surface—a pane of a door, a pane of stained glass, or even a panel in a comic strip—so it is not limited to windows. Glass panel is a more technical term used in construction and interior design; it may refer to larger sheets used in modern buildings and does not necessarily imply a window context. If you look through one section of a multi-part window, you are looking through a windowpane: each individual glass piece is a windowpane.
Formed from 'window' (from Old Norse vindauga, literally 'wind eye') and 'pane' (from Middle English pan, via Old French from Latin pannus 'piece of cloth'). The word took its modern meaning in the 17th century as glass sheets replaced smaller leaded panels in domestic windows.