The defender was replaced by Carlos Cuellar in the starting line-up for the 5-1 loss to Tottenham on Monday, but the manager says he was just rotating to freshen up the squad
The Republic of Ireland international was left out by Poyet for the 5-1 defeat at White Hart Lane, and the Uruguayan felt that because of the 32-year-old's stature at the club, that decision merited clarification.
"Because of the type of person he is, and the type of professional he is, he deserved an explanation," Poyet told reporters.
"I don't do that every week. Every time I make a change, I don't call the player to tell him, believe me. I've got no problem telling him if he wants to know, but I can't call a player in every time I make a change.
"But John deserved an explanation because of who he is, and how we need him."
Carlos Cuellar came into the side in place of O'Shea for his first start since November, and Poyet sang the praises of the Spaniard, despite the disappointing result.
"In my first two or three weeks here, Carlos was one of the players who understood exactly what we needed," he told the club's official website.
"He knows what I want and how we want to do it. He's very professional and intelligent, which is why he's played for so many years at the highest level.
"I needed to make a change and do something different. If I only refer to Carlos, he did well, though it's difficult to separate one player for the team.
"He did everything we asked for and credit to him for being ready to help us. The result wasn't the greatest, but it's nice to know we can count on him."