One hacky way to do this is using unordered lists and the keep_tex argument of pdf_document to itemize your code chunks, then adding [] to the \item portions within the LaTeX and then compiling it into a modified PDF.
First, here's my sample indent_chunk.Rmd file:
---
title: "Example"
output:
pdf_document: # Add this portion to your yaml header
keep_tex: true # to keep the .tex file used to create the PDF
---
#### Header
\hspace{0.8cm}no ordered list: code chunk doesn't work right now
# Create an unordered list with no text, indent your code chunk with 2 spaces so it becomes an item within your list
-
```{r}
2+2
```
When you compile the above, it will create the indented code chunks attached to a
bullet point.
Indented Code Chunk with Bullets
The next step is to open the indent_chunk.tex file that should be in your directory now.
The itemize code chunk should be preceded by \item, so following @Yarnabrina's advice, just change it to \item[].
\hspace{0.8cm}no ordered list: code chunk doesn't work right now
\begin{itemize}
\item # Add a [] to this portion of the TeX and re-compile the PDF
\begin{Shaded}
\begin{Highlighting}[]
\DecValTok{2}\OperatorTok{+}\DecValTok{2}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
## [1] 4
\end{verbatim}
If you're in RStudio, you should see a Compile PDF button on the source window. Clicking that will compile the document and your code chunk should now be indented.
Indented Code Chunk with no Bullet