I have just upgraded my Macbook Pro OS to El Capitan (v10.11.4).
My attempt to export a Markdown file (created using Sublime Text 2, v2.0.2, build 2221) to pdf using pandoc is now failing, and I receive the following error:
pandoc: xelatex not found. xelatex is needed for pdf output
My output command is as follows:
pandoc doc1.md -o doc1.pdf --toc -V geometry:margin=1in --variable fontsize=10pt --variable fontfamily=utopia --variable linkcolor=blue --latex-engine=xelatex -f markdown-implicit_figures -s
Above command worked like a charm prior to installing El Capitan.
FYI - in searching for questions here I have not found one that gives a suitable answer.
El Capitan's security features disable and remove the old symlink /usr/texbin. If you have MacTeX 2015, they should've been installed in /Library/TeX/texbin as well. You'll have to update the PATH your using to launch pandoc to include that folder. If you have a pre-2015 distribution of MacTeX, there are instructions here.