As of vSphere 5.5 VXLAN has its own vmkernel networking stack therefore ping connectivity testing between two different vmknics on the transport VLAN must be done from ESXi console with the following syntax:
vmkping ++netstack=vxlan <vmknic IP> -d -s <packet size>
or
esxcli network diag ping --netstack=vxlan --host <vmknic IP> --df --size=<packet size>
Thanks go to Ray Budavari for the hint.