This was answered a few years ago, I think pretty well. Essentially stomach acid travels with food or water into your intestines where another pump puts out a base that neutralizes the acid. I believe this is largely to avoid damage to the intestines which lack the protective goo that your stomach has. Instead, your intestines absorb different things at different places, letting the rest come out as waste. For instance, B12 is absorbed in the first part of your large intestine (source: I’m missing that section of intestine and have to get injections because I can’t get it from food or supplements.)
Anyway, second answer by rdavidson24 sums it up pretty well. https://www.google.com/amp/s/amp.reddit.com/r/explainlikeimfive/comments/67xfwe/eli5_how_does_my_body_filter_out_the_stomach_acid/
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