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The Owl-Eyed Man is similar to the billboard for Dr. T. J. Eckleburg with the "all-seeing" eyes. Both symbolize an uninvolved, spectator god. They watch all the activities of the humans struggling below, but don't comment on them or try to correct wrongs or lessen burdens. While Owl-Eyes does make a comment about Gatsby's real books earlier in the novel, he still provides Nick with no advice or significant knowledge about Gatsby. He simply makes his observation and leaves it up to Nick to draw his own conclusions.
His presence as one of the few people who actually attend Gatsby's funeral could demonstrate "God's" watching when humans are put to rest or could mean that in all his observing of Gatsby, he at least thought that Gatsby was worthy of his presence at his burial.