The girl, who signed her name as Faith, sent the letter after she accidentally broke the decoration while visiting a shop in Cambridge.
She stuck two £1 coins to the note, which she posted to the "Christmas Department" of the store.
Branch manager Dominic Joyce launched a bid to find the girl on Twitter using the tag £findfaith, saying he would like to thank her for the "adorable gesture".
John Lewis said the girl's parents had been in touch.
The letter read: "To John Lewis Cambridge. I'm sorry I broke a Christmas bauble on Saturday. It cost two pounds. Here is the money for it. Sorry again, Faith, aged 5."
Mr Joyce said Faith had clearly been well brought up.