If you're working in TurboTax Self Employed, you may see a tab called Personal instead of one for "Federal Taxes." Click on it and then select Personal Income, then scroll down to the income headings on the lower half of the page (you may have to click on "Skip to see all income in order to display them).
Under the Retirement Plans & Social Security heading, select IRA, 401k, Pension Plan Withdrawals (1099-R). Follow the prompts and you'll enter your 1099-R information. Once you enter it, TurboTax will ask you some questions, one of which will be What did you do with the money? You'll check the box saying I moved the money to another retirement account (or returned it to the same retirement account) and then another box saying I rolled over all of this money.
Checking those boxes will let TurboTax know that the entire amount is an indirect rollover and not taxable.
