Jacob tricked his brother twice; now the time has come to face him. His prayer to God at that moment reflects his sense of desperation:
O God of my father Abraham and God of my father Isaac, O Lord, who said to me, 'Return to your native land and I will deal bountifully with you'! I am unworthy of all the kindness that You have so steadfastly shown Your servant: with my staff alone I crossed this Jordan, and now I have become two camps. Deliver me, I pray, from the hand of my brother, from the hand of Esau; else, I fear, he may come and strike me down, mothers and children alike.1
His prayer is not just an expression of fear; it is also a realization. As the modern commentator Nehama Leibowitz notes, his prayer also reflects a sudden insight. As she explains, "Perhaps he still justified the immoral deed by the justness of the end, given the seal of approval in his father's confirmation of the blessing after the deed: 'yea, and he shall be blessed.' He had still not experienced even the shadow of a doubt regarding the rightness of his conduct. Only now through his prayer he experienced a re-appraisal of his conduct."2
Esau is angry, and rightfully so, for having been supplanted twice all those years ago. I would be angry too.
The Jewish philosopher Hermann Cohen argues that genuine morality is born when we understand how the other person feels. It is when we realize he hurts just like I do that we are able to make moral choices.
Jacob suddenly understands what he, himself, has done. And, as a result, he becomes a fully ethical being.
 This is the JPS translation.
 Nehama Leibowitz, Studies in Bereshit/Genesis, translated by Aryeh Newman, p. 364.