If you only got one IP on the server, there is no chance to do that. DNS is a simple name to number (IP) resolver. If you have two IPs on the server, you can point each subdomain to each of the IP-addresses and run both servers on the default port on each IP.
one.example.com -> 127.0.0.1 (server: 127.0.0.1:25565)
two.example.com -> 127.0.0.2 (server: 127.0.0.2:25565)