Besides it applying to the those singing the song, it is also defined as: A term African-American women use when they are talking about another female friend who they believe deep down thinks and believes what they do. Therefore its like they are 'sisters' by 'soul',and not by blood. I hope this helps you. Also, I wish to make needed correction in your question. It should be as such: What does "Hey, soul sister" mean? Also, the 'i" should be capitalized ( I ), in your sentence.

Hi, an alternative meaning (particularly in the context of the song) can be a playful reference to a female ....especially a female who enjoys music. Hope this helps :) Richard.