Google has updated its JavaScript SEO help document to add a new section on how to properly inject canonical link tags using JavaScript. The document says Google does not recommend using JavaScript for this, however "it is possible to inject a rel=canonical link tag with JavaScript."
The help document adds that "Google Search will pick up the injected canonical URL when rendering the page."
A note Google made is that "when using JavaScript to inject the rel="canonical" link tag, make sure that this is the only rel="canonical" link tag on the page. Incorrect implementations might create multiple rel="canonical" link tag or change an existing rel="canonical" link tag. Conflicting or multiple rel="canonical" link tags may lead to unexpected results."
Here is a code example of how to do this:
Previously, as Google is doing now, Google warned against doing it this way but did say it can work.
Forum discussion at Twitter.
