Your question implies that justice is one of William Golding's themes in Lord of the Flies, but that is an assumption which may not be true except in the reverse.

Consider some of the injustices found in this story: 

1. Piggy is one of the smartest boys on the island, but no one will listen to him (except Ralph, later when he is desperate) because of how he looks.
2. The little boy with the mulberry-colored birthmark is killed in a fire set by his peers.
3. Simon is the only one who understands that they are the beasts, but the boys kill him when he tries to give them this life-changing information.
4. Jack steals Piggy's glasses; however, when he goes to ask for them back, Jack allows Roger to crush Piggy with a boulder. 
5. Ralph has done nothing to Jack other than to offer the other boys a choice of leadership, yet Jack orders his tribe to kill Ralph.

The biggest injustice, of course, is that these boys were caught up in the middle of a world war and suffered drastic consequences because of adult incivilities and savagery.

In another sense, there is a kind of poetic justice which happens at the end of the novel. Ralph is rescued from imminent death (and the others from eventual death) by a naval officer who spends his days fighting life-and-death battles. At the end of the novel, 

Ralph wept for the end of innocence, the darkness of man’s heart, and the fall through the air of the true, wise friend called Piggy.

None of these losses speak of justice in any way, but they do reflect the injustices of a world in which the worst of human nature is displayed.