Google updated its JavaScript SEO best practices document with a new section on how to set the canonial URL when using JavaScript. Google wrote, "The best way to set the canonical URL is to use HTML, but if you have to use JavaScript, make sure that you always set the canonical URL to the same value as the original HTML."
So Google should figure it out but if it doesn't, don't blame Google. Google wrote:
The rel="canonical" link tag helps Google find the canonical version of a page. You can use JavaScript to set the canonical URL, but keep in mind that you shouldn't use JavaScript to change the canonical URL to something else than the URL you specified as the canonical URL in the original HTML. The best way to set the canonical URL is to use HTML, but if you have to use JavaScript, make sure that you always set the canonical URL to the same value as the original HTML. If you can't set the canonical URL in the HTML, then you can use JavaScript to set the canonical URL and leave it out of the original HTML.
Google explained, "Canonicalization happens before and after rendering, so it's important to make the canonical URL as clear as possible. With JavaScript, this means setting the canonical URL to the same URL as in the original HTML or if that isn't possible, to leave the canonical URL out of the original HTML."
Always test to make sure Google can process your JavaScript and one way to do that is to test it using the URL Inspection tool in Google Search Console.
Forum discussion at X.
