It seems like syntax highlighting in Jekyll is limited to using liquid tags and pygments like so:
{% highlight bash %}
cd ~
{% endhighlight %}
Markdown allows HTML, so if you don't mind adding a bit of JS, you could do this:
## A section
Here is some Ruby code.
puts "hello"
Then you could use Highlight.js (documentation here) to add highlighting based on that class.
It's not an ideal solution, but it should work with any Markdown parser.