Unique identifiers are a good option. However, they don't need to be used in game, only when writing and then reading the data from a save. Hopefully you'd already have some way to differentiating between entities you can use, otherwise you can make something up (typically an int or long)
Pick a unique ID for each entity, then proceed to writing the entities. For each entity, write its ID and when you write its components, add that ID as a header to the component information. Also write the ID for any target info. Then, when you're reading back in, you can use something like a dictionary to store the entities in, referenced by their ID. Then when you read a component, you can get the ID and index into the dictionary and add that component to that entity.
When I read and write entities, I write all of the entities first, without their components. This makes it much easier when reading in the components later because you have all the entities available to you. It avoids the situation where you're reading in an entity that has a component that targets another entity, but you haven't created that target entity yet because it's deeper in the file.
