Creating a million tcp connections from one host is non-trivial.
The key words being "from one host". With a single client machine connecting to a single server endpoint, the (src ip, src port, dest ip, dest port) is reduced to being unique only on src port (from the client's perspective), so that's where the 65k limit, and the need for more IPs to do that, comes from. Using multiple source IPs on the same machine is like using multiple client hosts.
...using IPV4 there is a hard limit of the short integer used to indicate the port number which automatically limits you to 65536 connections (actually a few less, usually you'll lose 3 for stdin,stdout and stderr (which you can close to reuse them) and one for the listen socket).
The file descriptor limit is independent of the 65k total possible source ports. The source port limit is part of TCP/UDP. The file descriptor limit is set by ulimit (nofile in limits.conf) on a per-process basis and in /proc for system-wide. If you need more file descriptors, you can reuse 0, 1 and 2, but that's going to free up some ports so a single process can make more connections to the same server endpoint.
edit: You may be limited by number of open sockets or file handles. It's likely a per-process limit. Google or some linux guru could help you track down what limit it actually is, but it's not the number of server ports available. It might be a number you could raise.