Generally speaking, that's exactly what the
:noautocmd command modifier is for. Just prefix your command with that and all autocommands should be disabled for just the run of that command.
Of course, this is the scorched earth approach. If there are other autocommands that you need to keep enabled and you're trying to ignore just the one you mentioned than a different approach is required. If this is the case I'd suggest explicitly mentioning it in your question, though there are few things I can mention right now...
First, want to see which, if any, autocommands are being run? Try this:
Speaking for myself, I have two plugins that have actions that are triggered by an autocommand associated with
:w. They aren't what I'd call critical but I may still want to keep them intact. They are not associated with
BufWritePre, though, so for me an alternative to
:noautocmd would be to disable just the
BufWritePre event, do the write, then re-enable that event:
:set eventignore+=BufWritePre | w | set eventignore-=BufWritePre
That could easily be wrapped up in a mapping or user command.