The rules for the employer are to withhold SS taxes, without regard to whether or not you have hit the limit with another employer. Or do you really expect employers to take the word of an employee who says, "you don't need to withhold any SS taxes, because I have already hit the limit with another employer"?
"My employer knows that I have hit the SS limit during the first W2 so they correctly did not withhold on the second." The employer may have known this, but they did not "correctly" withhold on the second W-2. The fact that the employer had reason to know that you had exceeded the limit is the exception and not the rule.
Then, at the end of the year on your tax return, you will get the excess SS taxes refunded on your tax return.
Since I don't think you will be able to e-file like this, may I suggest (unless one of my compatriots has a better idea), that you split the amounts in boxes 3 and 4 between the two W-2s. Yes, this won't match what the IRS has, but it will hopefully get you past any e-file rejects, and if the IRS writes you a letter, you can just respond that the second employer did not withhold SS taxes correctly, and this was your workaround to be able to e-file.
Since the IRS really really really wants you to e-file this year, I don't think it will go beyond this.
@chrisf2
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