The War for American Independence may be the closest the U.S. has ever been to a "just war". Dern noted that it may not be a just war because the revolutionaries did not comprise a sovereign state, thus breaking one of the tenets of the theory.
At the time, there were two views to sovereignty:
1) The old view -- the King is the absolute ruler, and;
2) The new view, based on Locke's natural law philosophy, the Scholastics, the and republican models of Greece and Rome -- the people and the ruler are in contract. If the ruler grossly violates the contract, he loses the right to rule.
I think The Declaration of Independence came before all the fighting (if not I'm sure they sent plenty of letters explaining their complaints). In effect, the revolutionaries announced their sovereign state and kept the tenet in question.