It means Pedro will have been dropped for the final two games of the season due to a training ground ruck with teammate Jan Paul van Hecke. He was also axed for this week's win against Liverpool.
Brighton boss Fabian Hurzeler explained: "With Joao we had a small issue in training, the type which isn't uncommon from time to time in all football clubs. We dealt with it internally and the matter is closed.
"Joao is an incredible football player, he's a match-winner for us, he's a great player and that's why we invested in him.
"But there are principles that are non-negotiable and count for everyone - that everyone has to stick to - where we don't make any compromises.
"Joao is still a young player. He will grow and I'm sure he will learn from this and come back stronger next season. I'm really looking forward to seeing him renewed and reinvigorated at his highest peak."