The correct way to handle this (and quite frankly, any javascript functionality) is to build it to work without javascript (keep the pagination), then have the javascript remove the pagination and implement infinite scrolling. This ensures that visitors with JS disabled get the full experience of the site, search engines can easily crawl your full catalog, and users with JS enabled get the "enhanced" experience you desire from a UX standpoint.
It's not an "either or" scenario. You can absolutely have an easily indexed site that extensively uses JS.