Commander has only short organ (5)
I believe the answer is:
colon
'organ' is the definition.
(colon is a kind of organ)
'commander has only short' is the wordplay.
'commander has' becomes 'co' (I am not sure about this - if you are sure you should believe this answer much more).
'only' becomes 'lone' ('lone' can be a synonym of 'only').
'short' means to remove the last letter.
'lone' with its last letter removed is 'lon'.
'co'+'lon'='COLON'
Can you help me to learn more?
(Other definitions for colon that I've seen before include "Punctuate part of the large intestine" , "Part of the intestine - punctuation mark" , "cash" , "City at the Caribbean entrance to the Panama Canal" , "Stop (less than full)" .)