The Whonix Gateway can be used as a tor router for any virtual machine, including Kali Linux! Here is how to setup Whonix and Kali so that Kali Linux is completely routed through Tor.
Install Kali Linux in Virtualbox, and perform updates (sudo apt-get update && sudo apt-get upgrade) then shut down the VM.
Download and import the Whonix Gateway Virtualbox appliance into Virtualbox. Only the gateway is needed.
Start the Whonix Gateway and proceed with the initial setup then perform any OS updates (sudo apt-get update && sudo apt-get upgrade). A reboot is generally required after the initial setup.
Leave the Whonix Gateway VM up and running. This is what will be used to connect to tor!
Next, edit the Virtualbox network settings for Kali Linux. Set Adapter 1 to Internal Network, and Whonix.
Boot Kali Linux and edit the relevant network settings.
Add the following to the bottom of /etc/network/interfaces
iface eth0 inet static address 10.152.152.11 netmask 255.255.192.0 gateway 10.152.152.10
Replace the entire contents of /etc/resolv.conf with the following:
Bounce the interface inside Kali:
sudo ifdown eth0 sudo ifup eth0
Verify that Kali is using tor via the Whonix gateway by visiting a page inside Kali such as:
https://check.torproject.org or https://icanhazip.com.