Ronaldo was seen leaving the bench before the end of the 2-0 win over Spurs on Wednesday and later left the stadium before Ten Hag and the United squad had returned to the dressing room.
Speaking at a news conference on Friday, Ten Hag confirmed Ronaldo refused to come on as late substitute in the game, prompting the manager to drop the 37-year-old from the squad to face Chelsea on Saturday.
Asked whether Ronaldo refused to come on as a substitute against Tottenham, Ten Hag replied: "Yes."
"I am the manager and I am responsible for the top sport culture here and I have to set standards and values and I have to control them," he added.
"We are a team and in the team, we have values and standards and I have to control that. After Rayo Vallecano, I told [him] it was unacceptable but he was not the only one, but that is for everyone so when it's the second time, there will be consequences.
"I sent a warning at the start of the season, next time there has to be consequences. Football is a team sport and you have to fulfil certain standards. And I have to control it."
Ronaldo trained alone with fitness coaches on Friday and won't be part of the squad for the game against Chelsea at Stamford Bridge on Saturday.
He is expected to rejoin the main group on Monday ahead of the Europa League tie against FC Sheriff at Old Trafford on Thursday and Ten Hag said the Portugal forward remains "an important player."
"The talks are between Cristiano and me," said Ten Hag, who will also be without Anthony Martial against Chelsea as he continues his recovery from a back injury.
"We will miss him tomorrow. It's a miss for the squad but it's important for the attitude and mentality of the group and now we have to focus on Chelsea as that is important. He remains an important part of the squad."