Yes - I replaced my factory cloth seats with Classic Soft Trim leather replacements and they fit perfectly.
I didn't actually install mine. Classic Soft Trim won't sell you the seats without an install, at least that's how the branch here was. Check out this thread, where one member outlines his install of leather:
http://www.toyota-4runner.org/4th-gen-t4rs/74407-leather-install.html