[This post is based on the SharePoint 2016 Preview — Functionality is not guaranteed to be supported, configured identically, or exist in RTM]
$farm = Get-SPFarm
$wa = Get-SPWebApplication http://webAppUrl
$wa.WebService.SideBySideToken = $farm.BuildVersion.ToString()
$wa.WebService.CdnPrefix = "static.sharepointonline/bld"
$wa.WebService.EnableCdn = $true
Using Fiddler, browsing to a home page, you should now see requests to http://static.sharepointonline.com/bld/_layouts/15/16.0.4316.1217/init.js, as an example.
You can also configure your own personal CDN using the same method. As long as the CdnPrefix does not contain “static”, you do not need to set a SideBySideToken value.