New pandoc version have made this easier since my original answer. According to pandoc's manual, you can now specify classoptions directly in the YAML front matter:
---
classoption:
- twocolumn
---
The new div notation also allows for inserting two column sections anywhere in the document, working for most formats
:::::::::::::: {.columns}
::: {.column width="40%"}
contents...
:::
::: {.column width="60%"}
contents...
:::
::::::::::::::
Original answer
You can use the article option twocolumn
to format the whole document in two columns. Add this to your yaml front matter:
---
output:
pdf_document:
pandoc_args: [
"-V", "classoption=twocolumn"
]
---
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