最後の2文字の文字列で並べ替え

これを試してください：

SELECT port 
FROM interfaces 
ORDER BY SUBSTRING_INDEX(port, '/', 1), CAST(SUBSTRING_INDEX(port, '/', -1) AS SIGNED)

SQL FIDDLE DEMOを確認してください

出力

|   PORT |
|--------|
|  Fa0/1 |
|  Fa0/2 |
|  Fa0/3 |
|  Fa0/4 |
|  Fa0/5 |
|  Fa0/6 |
|  Fa0/7 |
|  Fa0/8 |
|  Fa0/9 |
| Fa0/10 |
| Fa0/11 |
| Fa0/12 |
|  Gi0/1 |
|  Gi0/2 |
|  Null0 |
|  Vlan1 |