The question behind the question is "Why do we practice scales?" And there are a lot of reasons. I hope it's not disappointing, but you don't stop when you've "learned" a scale; they'll be an important part of your practice all your life. What you mean by "learn" is "I've mastered one of the standardized finger patterns for scales in certain keys," but scales will be something you practice long after you've memorized these patterns.
So why practice scales (and arpeggios)? The usual explanation is one you already noticed: because you find them in "real music." For an example from my instrument, violin, Carl Flesch's scale book includes sections in octave double stops, and includes arpeggios of various chords. So if I've practiced a G diminished arpeggio in octaves, then when I hit this bit of the Mendelssohn violin concerto...
... then I know just what to do.
There's already been some speculation in the comments that scales and arpeggios don't make up that much of the music we play; I'd counterargue that they do, especially when we count arpeggios (and chromatic scale). In particular, we're all supposed to know scales so well that we can rip straight through them much faster than other passagework. From later in the same concerto, I'd better be used to where I shift in a B major scale...
But if the argument is "hey look, that's just a couple of measures out of an entire concerto; why waste time studying scales and just learn the 'real' pieces," then I'd point out that the scales and arpeggios are the parts that I can "take with me" to some other piece, and the thematic material is unique to each piece.
But besides the "because you'll use them" argument, scales make a convenient "abstract" way to practice lots of techniques. We don't have to think hard to remember which note comes after which in a scale; they're familiar and simple. So they make a good medium in which to practice, say, getting louder or softer, or playing longer or shorter notes, slurring pairs of notes or three notes, and even rhythm patterns. They make great warm up material, in which you can get both your brain and your fingers "up to speed" with something familiar.
So to your actual question, "why learn the minor scales if I've already learned the major fingerings and they contain the natural minor"... well, as you can guess, my answer is that it isn't even about "learn," it's about "live with." But even if the immediate goal is to master certain finger patterns, consider this: If you start a C major scale with your 1st finger (thumb), then the A is probably 3rd finger. But the standard fingering of an A minor scale would start on 1st finger. So if the immediate goal is to memorize fingering patterns, then the minor scales would have their own.