"Upon" is just a very formal or poetic substitute for "on". The meaning is the same, but the tone is different.
casual/neutral: I put the glass on the table.
formal/poetic: I put the glass upon the table.
VERY formal/poetic: I set the chalice upon the table.
casual: He looked at her with love in his eyes. He decided to walk up to her and ask her out on a date.
formal/poetic: he gazed at her with love in his eyes. He hoped that one day he would be worthy of asking her out.
very formal: he gazed on her with love in his eyes. She was the woman he had always dreamed about, but he doubted he would ever be brave enough to talk to her.
VERY VERY formal and poetic: he gazed upon her with love in his eyes. She had become his whole universe, and he would never think about anything else ever again.
Shine on us, Infinite Tsukuyomi= Tsukuyomi, you are like the sun.
Shine upon us, Infinite Tsukuyomi= Tsukuyomi, you are like the god of light. You are what brings light to the universe.