Saying "잘자요" back is probably not common.
Most people would at least add 네 as in "네, 잘자요".
There can be other responses depending on what's on your mind, etc.
- 네, (XX 씨도 / 언니도 / 선배도 / etc) 편히 쉬세요. => Ok, you have a good rest too.
- 네, (...) 좋은 꿈 꿔요. => Ok, you have a good dream too.
- 네, (XX 씨도 / 언니도 / 선배도 / etc). => Ok, you too.
- 네, 내일 봐요. => Ok, see you tomorrow. (if that is the case)
- 네. => Ok.
- 그래요. => Ok.
If you don't have anything particular to say, just 네 or 그래요 is also okay.