When you enter the 1099-R, there are several screens that follow. On the screen with the heading "What did you do with the money from [plan name]?", check the line with "[your name] moved the money to another retirement account (or returned it to the same retirement account)". No, this is not obvious.
Checking the top will expose three new lines. Check the box "[your name] did a combination of rolling over, converting, or cashing out the money".
This will expose two new boxes. in the top box ("Amount rolled over to another (or back to the same) retirement account"), enter the amount of the distribution that you put back in the IRA. This part will appear on line 4a but not 4b on the 1040 because it will not be taxable.
The rest of the distribution will appear in line 4b as taxable.
[Edited 4/13/2020 2:39 pm - corrected typo]
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