I start to go crazy when I try to think of lyrics like this. I know it's not arbitrary where the artists decide to break the lines, but most lyrics lack the clarity of an end-stopped poem where punctuation lets us know which clauses go together.
For me, this would all make sense with some punctuation.
Everything was ugly, but your beautiful face left me no illusion.
(Here it sounds like the beautiful face is not a part of the "everything." It could be a memory he's having in the midst of everything ugly. That memory of the beautiful face makes it impossible for him to find beauty among all the ugly stuff.)
Everything was ugly but your beautiful face, (and it) left me no illusion.
(Everything was ugly except your beautiful face, and it made it impossible for me to see everything else as anything other than ugly by comparison.)
Those are the only two meanings of the line I can sense here.
Then again, it's possible that Bono just liked the sound of "left me no illusion" after the beautiful face part and didn't care if it was syntactically.