While both of these tools are used to make edits to the application, there is a fundamental difference between the two. The Adobe premiere pro is a video editing application whose emphasis is on editing video clips. To this end, it has tools that complete editing tools that can input necessary modifications for both Audio and video. While in the case of Adobe After effects, it is used to implement digital motion graphics, special effects, shapes, 2D animations to an already established video file. One can say that the premiere pro is a pre production tool and After Effects is a post production tool.
The difference between the two is one of the main reasons that video editors employ both these applications on the same video file.