"IP Protocol 41" is one of IPv6-over-IPv4 encapsulation.
This article describes how to configure the right service which can be applied to NSX vDefend firewall to control this kind of traffic.
VMware NSX
VMware vDefend Firewall
To control the "IP Protocol 41" traffic, Either create a new service or use Raw Porto-protocols by select "service type" as "IP" and "additional properties" as "IPv6".
Then apply them as the "services" in NSX firewall rules.
Eg. for Services
For Raw Port-Protocols
Below is an example in lab which the "allow" rule use the customized service and the "deny" rule utilize Raw Port-Protocols.