Just to be clear, I’m not saying this to criticize you — it’s just that I find it a bit strange that a god could lose to a mortal. That said, I haven’t mentioned the Tree of Life yet.
You are correct, Yukine is indeed a God though for reasons (Some mentioned in the story so far and others not mentioned yet) he is extremely weakened at the moment. His god-like power has been watered down easily by 80-90% of what it actually is. There is also a lot more about the mortal he was fighting that will be revealed in later chapters.
There will be more that is revealed about Gods in future chapters.