TL;DR

Use ethtool to locate a physical network port by blinking the lights:

sudo ethtool --identify eth0

Details

On systems with multiple physical network adaptors, it is not always obvious which physical port belongs to the software interface. For example, the following desktop has multiple network interfaces:

jemurray@desktop:~$ ifconfig -a
eth0      Link encap:Ethernet  HWaddr 78:e3:b5:06:91:18
          inet addr:192.168.86.123  Bcast:192.168.86.255  Mask:255.255.255.0
          inet6 addr: fe80::7ae3:b5ff:fe06:9118/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:9613 errors:0 dropped:172 overruns:0 frame:0
          TX packets:1256 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:798122 (798.1 KB)  TX bytes:338757 (338.7 KB)
          Interrupt:95

eth1      Link encap:Ethernet  HWaddr 78:e3:b5:06:91:19
          BROADCAST MULTICAST  MTU:1500  Metric:1
          RX packets:0 errors:0 dropped:0 overruns:0 frame:0
          TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:0 (0.0 B)  TX bytes:0 (0.0 B)
          Interrupt:99

eth2      Link encap:Ethernet  HWaddr 78:e3:b5:06:91:1a
          BROADCAST MULTICAST  MTU:1500  Metric:1
          RX packets:0 errors:0 dropped:0 overruns:0 frame:0
          TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:0 (0.0 B)  TX bytes:0 (0.0 B)
          Interrupt:103

eth3      Link encap:Ethernet  HWaddr 78:e3:b5:06:91:1b
          BROADCAST MULTICAST  MTU:1500  Metric:1
          RX packets:0 errors:0 dropped:0 overruns:0 frame:0
          TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:0 (0.0 B)  TX bytes:0 (0.0 B)
          Interrupt:107

The ethtool command has an --identify option that blinks the lights on a physical network interface.

Before the ethtool command is run:

Using ethtool to locate the port:

sudo ethtool --identify eth0

Unfortunatly, not all hardware supports identification:

jemurray@server:~$ sudo ethtool --identify eth0
Cannot identify NIC: Operation not supported