Form 1120S was rejected because it was late, but how can I file the election and have my return rejected at the same time?

you should be able to e-file without paying the penalty. the IRS will bill you. there's no way to pay the penalty when you e-file. when you get the bill, you may want to request abatement if this is the first time you filed an S-corp. if not, you may request abatement if you have reasonable cause for filing late.