^Also qualification to AFC Cup group stage if failed to qualify for the AFC Champions League group stage.
^Since the winners of 2016 Piala FA, Johor Darul Ta'zim, currently qualify for AFC Champions League based on their league position, the spot awarded to the Piala FA winner (AFC Cup group stage) would be passed to the next best team in the table (in this case, the second-placed team).
^Kedah Football Association (Kedah FA) has been found guilty of putting the suspended player during the match against Pahang on August 3, 2016. Therefore, the Football Association of Malaysia (FAM) has been awarded 3 points for Pahang and Kedah sentenced deducted 3 points for the incident.