Here is a little explanation of it. While it is not straight from Square Enix, it is written on a wiki...

http://ffxiv.consolegameswiki.com/wiki/Morale

"Morale is an attribute that affects the amount of damage you take from enemy players and the amount of damage you deal to enemy players in PvP. The attribute only comes into play in level 50 PvP matches, where it replaces Defense and Magic Defense in influencing the damage you receive."