Jumping is basically the same as a side-scroller, just the camera position is different. When the user presses jump you add a certain amount of y velocity, and then every update you add gravity to the velocity, and update the player position. It works the same in 2D or 3D basically.
See this example I posted a little while ago. It's for a 2D sprite so try it out (the logic is the same even with 3D or different camera angles).
https://godotforums.org/discussion/comment/31028/#Comment_31028
