It seems like syntax highlighting in Jekyll is limited to using liquid tags and pygments like so:
{% highlight bash %}
cd ~
{% endhighlight %}
So I ran into this problem as well and after banging my head around a lot of places finally realised with official redcarpet2 support in Jekyll this is pretty simple. Write this in your _config.yml
# Conversion
markdown: redcarpet
highlighter: pygments
redcarpet:
extensions: ["no_intra_emphasis", "fenced_code_blocks", "autolink", "strikethrough", "superscript"]
Make sure that you have pygments css file and it is included. THIS STEP IS IMPORTANT.
You can read my blog post http://blog.championswimmer.in/2015/10/jekyllsyntax-highlighting-in-github-favoured-markdown-codeblocks/ for details.