With the Veeam Community Edition you can backup till 10 VMs and you can choose between using the Veeam Agent or the Veeam Standard backup method. As you have ESXi Free you will have to chose Veeam Agent so the backup transfer will be from the VM to the repository without interacting with the Hypervisor.
This is a really powerful tool and I recommend it 100%. Of course if you have more than 10 VMs you can also use the Veeam Agent for Linux or for Windows Free with their limitations.