Sure! I use pandoc to render Markdown, but you can use whatever Markdown processor you like in place of pandoc.

Makefile

    all: example.html

    example.html: example.md example.png
        pandoc $< -o $@

    example.png: example.dot
        dot -Tpng $< -o $@

example.dot

    digraph G {
        foo -> bar;
    }

example.md

    # Example

    ![example graph](example.png)