You must include form 5329 when you e-file and Unfortunately this can only be done using the "Forms" mode which is only available with TurboTax CD/Download if you do not have a 1099-R to file.
You can change to TurboTax Basic CD/Download if you choose.
Once this is completed here are the steps to add Form 5329 to your return.
You will not pay any penalty now until the IRS determines if it will grant the waver, then they will inform you if you owe the penalty.
Alternative for TurboTax Online: Print, complete and mail Form 5329 by April 18th since it is a signature form and can be mailed separately (click the link for form and instructions).