If you retrieve an entity, for example using the findOne method call within a transactional method it has become managed from that point by the persistence provider.
Now if you make any changes to that entity (which is actually a proxy object), upon transaction commit, those changes will be persisted to the database, regardless of the fact of invoking the save or update methods.
save or persist has to be used when you are creating a new entity from scratch and persistence provider does not know of its existence yet.
Remember that you can prevent making any changes upon commit, if you use detach or evict methods on that particular entity before those changes occur.