The clash took place after Blues' 3-2 defeat at Newcastle this month.
A Chelsea source revealed: "Benitez blamed JT for two of the goals. He blamed him for losing Jonas Gutierrez for Newcastle's first goal and for diving in without winning the ball in the build-up to their second."
Benitez let fly at JT in front of his shocked team-mates - and the Blues legend blasted back. The source added: "The manager was furious after losing in the last minute and made it clear he wasn't happy with John's performance.
"He also reckoned that John wasn't fit enough after three months out of action.
"JT wasn't happy about the criticism and had a go back at the boss in front of all the other players in the dressing room.
"Everyone was stunned by the way the manager singled out JT. It was not the way he is usually spoken to at Chelsea."