You are supposed to be able to. It is the IRS' preference. (Technically, they require it to be e-filed if the original was e-filed). However, that is dependent as much as anything on the software you are using. TurboTax Business does not support e-filing of a superseding return. If this is your case, you would need to print out the return and write "Superseding Return" across the top of the front page of your 1120-S. Mail in the return (and attach an explanation of the changes), along with all attachments as if you were otherwise filing an original return. There is no X (amended) form that corresponds with Form 1120-S.
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