There are three options:
:noa[utocmd] w[rite]
will save without starting any auto-recordings. Unless you have other settings / plugins using autocmds, this will be fine.
:set eventignore=BufWrite | write | set eventignore=
temporarily disable the event BufWrite.
Alternatively, you can also add a conditional expression around your autocmd:
au BufWrite * if ! exists('g:no_autoformat') && index(blacklist, &ft) < 0 | :Autoformat
autocmd :let g:no_autoformat = 1.
PS: :autocmd | endif.