Victory in the FA Cup final has seen Palace earn a place in the competition, though that spot is under threat due to UEFA's multi-club ownership rules.
Palace minority shareholder John Textor owns Lyon, which have also qualified for the Europa League next season.
Palace are now in talks with UEFA about the situation and Eze said: "I really hope that that's not the case (removed from the Europa League) and I hope that Palace do get the reward for that (FA Cup win), because of what it took to actually achieve it.
"It would be a huge shame if that was the case, but I'm trusting that it will work out in the end.
"I'm sure it will work itself out and it should work itself out, because there are players who have worked to be in this position.
"There are fans who have been with the team throughout the whole season and experienced everything.
"It would be unfortunate, but I'm positive that it won't be the case."