How helpful is it for PhD admissions to be second author of a paper in a recognised journal? I recently submitted a paper to a fairly well-known journal and it got accepted. I'm listed as the second author. I'm a master's student. How much prestige is associated with this if I apply for a PhD?
This is a normal and expected thing for graduate students to do.  You should definitely list it on your CV and make it visible in your application to PhD programs and it will be a positive factor.