The cables are slightly different in design, but the main difference is that they have different maximum frequency of operation: 100MHz for CAT5 (or CAT5E) and 250MHz for CAT6. None of today’s applications (except for esoteric video stuff) actually use as much as 250MHz of the frequency range, so the main reason to use CAT6 is to (try to) provide support for future applications without the need to install new cables.
Directly answering your question: yes, you can use CAT6 in place of CAT5 if you have to. Not vise versa though.
Dmitri Abaimov, RCDD