How do I make a reference to a figure in markdown using pandoc?

You can use the pandoc-fignos filter for figure numbering and referencing. It works with any output format -- not just LaTeX.

Add a label to the image's attributes like this:

 ![Caption.](image.png) {#fig:description}

... and then reference the figure like this:

 @fig:description

Information on how to install and apply the pandoc-fignos filter is given on its Web page. There is also the pandoc-eqnos filter for doing the same kind of thing with equations.

In pandoc you can even do:

![This is the caption\label{mylabel}](/url/of/image.png)
See figure \ref{mylabel}.