In my case, I've gotten through 40 years of performing with jazz groups, so in some sense I'm doing OK, but I also know that I struggle with ultra-modern jazz harmonies. This came into pretty sharp relief when I played with some musicians who were composing all of their own tunes. I reach the end of my mental map, and then I have to fake it, or improvise directly from the melody.
But I agree that "ear" and perception of harmonic structure are closely related. It's hard to describe, and might make a psychologist cringe, but a musician develops a "mental ear." And I wouldn't recommend my approach to a young player. Most people want to become proficient in fewer than 40 years. ;-) There are things I can't do. I can't compose or arrange anything worth playing. Without exception, every musician I've played with who could compose or arrange decent jazz material has a music degree.