How can I specify rmarkdown to use python3 instead python 2?

You can add engine.path = '/path/to/python3' to override the python (2) executable. For example,

---
title: "python"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{python}
import sys
print(sys.version)
```

```{python, engine.path = '/usr/bin/python3'}
import sys
print(sys.version)
```

---

You can select your desired python version, as default, with an R chunk:

```{r setup, echo=FALSE}
library(knitr)
opts_chunk$set(engine.path = '/usr/bin/python3')
```

From now on your python chunks will use Python3:

```{python}
import sys
print(sys.version)
```

This way to select python version avoids to add the engine.path variable to every code chunk.