Ten Hag has taken the decision after Ronaldo left Old Trafford before the end of the 2-0 victory over Spurs on Wednesday.
Ronaldo did not train with the first team squad Thursday and is not expected to rejoin the group until Monday.
Sources have told ESPN that the club have backed the action taken by Ten Hag but insist the 37-year-old remains "an important part of the squad."
A club statement issued on Thursday read: "Cristiano will not be part of the Manchester United squad for this Saturday's game against Chelsea. The rest of the squad is fully focused on preparing for that fixture."
Ronaldo left his seat on the bench to walk down the tunnel before the full-time whistle against Tottenham, despite Ten Hag having two more substitutions available.
Sources also told ESPN that Ronaldo left the stadium and was not in the dressing room when Ten Hag and the players returned.
Ronaldo reported to United's Carrington training ground at around 10:30 a.m. on Thursday.
He held talks with Ten Hag before the Dutchman decided to drop him from his squad to face Chelsea at Stamford Bridge.
Following his axing from the squad to face Chelsea, Ronaldo wrote on Instagram that the "heat of the moment" had got the best of him and that he would work hard to return to the team.
"I've always tried to set the example myself for the youngsters that grew in all the teams that I've represented," he wrote.
"Unfortunately that's not always possible and sometimes the heat of the moment get's the best of us.
"Right now, I just feel that I have to keep working hard in Carrington, support my teammates and be ready for everything in any given game.
"Giving in to the pressure is not an option. It never was. This is Manchester United, and united we must stand. Soon we'll be together again."
It is the second time Ronaldo has been reprimanded by Ten Hag for leaving a game early.
The United boss branded his behaviour "unacceptable" after he was pictured leaving Old Trafford before the end of a preseason friendly against Rayo Vallecano in July. Ronaldo started the game but was substituted at half-time.
Ronaldo was also captured shaking his head after Ten Hag's decision to substitute him during the second half of the 0-0 draw with Newcastle on Sunday.
The Portugal international is keen to leave the club after starting just two Premier League games. He has scored two goals in 12 appearances so far this season, including his 700th club career goal in the 2-1 win over Everton earlier this month.