He can't quite explain how he 'knew' the other would be upset. If he thought about it he'd assume it was their friendship, their closeness, so on. Either way, he holds the other close now, Suzu herself apparently somewhat resigned to watching them be 'upset'.

"...It shall be alright, Yuuya," Gongenzaka whispers, doing his best to reassure the other of what he's saying. "I, the man Gongenzaka, promise that. ...We shall get through this..."