Darkseid clearly states as he uses his omega beams on the league that he is going to inflict his punishment on them. Specifically being banished to another dimension. Later the league discuss why they are in the "other dimension" and not dead from Darkseid's omega beams. They theorize that the mother box may have saved them ignoring Darkseid's own words that he was banishing them to another dimension. In order to compound the error Darkseid himself is surprised the justice league is still alive as they approach him for the final battle.