I am not familiar with such an intentional change.
I googled -
file:pdf
I went to the first result -
And the internal PDF viewer was used to render the PDF.
I am using Chrome 59 (not 58), though. Try updating your Chrome.
Or maybe when you downloaded it, you (or someone else using your browser) selected "Open with system viewer" once (in the context menu of the download) and it might have persisted. Select it again in order to uncheck it.
(You might have also selected to open it automatically when done, so in order to revert that choice, or the previous choice I mentioned, you should probably look for a big PDF file to download, because then it will be displayed in the downloads bar long enough for you to uncheck either of those options)