If my memory serves me correctly, you totally can. You'll want to create a base node and label it with meaningful name, like GameOverNode, in the game scene.
Then you add the user interface nodes that you want as a child of it. To create the popup effect you'll want to make the GameOverNode hidden. When you want to show the game over popup, set it to not hidden.
Tip: When you add the user interface nodes you may want to set them up so they're off screen. That way when you show the GameOverNode you can animate all the sub nodes into screen.