Open TurboTax and log into your return. Since you have filed, you should be asked if you want to amend. Answer "yes".
When you get into the return, do a Search for 1099-r (lower case) and jump to it. You should see a table of 1099-Rs (I guess there have to be at least two on your return).
Use the Delete button to delete the duplicate 1099-R.
Go to the Federal Review and filing steps. You want to print forms 1040X and 1040 (and any other forms that changed).
Sign and mail the set of forms to the IRS.
Please see this TurboTax FAQ for details on how to amend your return
with TurboTax - https://ttlc.intuit.com/replies/3288565