Cohen's Ballad of the Absent Mare is the most spiritual rock and pop song I have encountered because it describes the full path rather than certain aspects.
This song may be regarded as presumptuous: God talking directly to Leonard Cohen. We can also read a very humble attitude from the lyrics.
Anthem, released in 1992 on the album The Future, is among the first songs that come to my mind when asked about a song with a spiritual core message.
Different Sides was released in 2012 by then 78 year old Leonard Cohen on the album Old Ideas. I particularly like this song because it addresses an issue I find crucial on my spiritual journey.