The 35-year-old has missed the club's last two games with an ankle injury, but was hopeful of returning in time for this weekend's match at the Emirates Stadium.
"John is working but he didn't recover for the game against Arsenal. In this case it is important [to listen to] what the player feels and the pain he is in," Conte told reporters.
"We have three central defenders and it is normal to make a choice. It is a big game between two big rivals and it is important to play a good game. We know we face a good team."
Chelsea are looking to bounce back from their first competitive defeat under Conte, which came at the hands of Liverpool on Friday night.