It is too late to fix the error. So just complete 1040 Form and calculate federal incoming tax, return the Dorm 1040 with your payment check (Contact the pay-roll dept. of your company to obtain the value that how much the social security tax you should pay, and minus this amount from your incoming value, then calculate tax). Also attach a check for social security tax payment. Attach also a note to explain the reason that why you did not pre-pay the tax. Maybe the IRS won't fine you.
BUT I can not be sure whether it is a possible method.