If I understand the longtable documentation correctly you'll have to modify Pandoc's LaTeX output manually, i.e. instead of letting pandoc handle the LaTeX → PDF step behind the scene you must convert Markdown to a LaTeX file:
``` shell
pandoc document.md -o document.ltx
```
then open the LaTeX file and look for where it says something like
``` latex
\begin{longtable}[]{@{}ll@{}}
\caption{My caption text}\tabularnewline
\toprule()
dolores & culpa \\
\midrule()
\endfirsthead
\toprule()
dolores & culpa \\
\midrule()
\endhead
```
(Typially you would search for the caption text. If that contains lots of formatting you may want to insert some unique "word" into the caption in the Markdown source, search for that in the LaTeX source and then delete it in the LaTeX source.)
and insert
``` latex
\caption[]{(Continued from previous page)}\tabularnewline
```
just below `\endfirsthead`.
then do
``` shell
xelatex document.ltx
```
substituting your LaTeX engine of choice for `xelatex`.
Disclaimer: I don't have any texlive installation to hand to test this on ATM because I'm 40 km from my laptop. Also it is ages since I needed to do anything like this manually and I don't remember how I did it. This is my best shot ATM. Please let me know how it goes!