I have seen some journals that ask that you put figure captions all together on a single page separate from the figures themselves (an extremely annoying requirement both for reviewers and authors). But I doubt that is what your journal is asking you to do.
More common is just that you put each table and figure on a separate page. So the caption would appear below (or possibly above) the figure. Both the caption and figure would be on the same page. And that page would be at the end of the manuscript. This is standard in, for example, APA style. See this annotated sample manuscript.
So to answer your specific question the image file is commonly embedded in the document, and the image file would not include the caption. The caption would be standard text from latex, MS Word, etc. and only the figure component would be an image file.