The 37-year-old was an unused substitute for Manchester United in their 2-0 win over Tottenham on Wednesday, but raised eyebrows by walking down the tunnel in the 89th minute before reportedly leaving Old Trafford early.
He also showed his displeasure at being substituted during their 0-0 home match against Newcastle last Sunday.
After the match against Tottenham, Manchester United manager Erik ten Hag said he would "deal with" the issue on Thursday.
In a statement, the club said: "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 has started only two games this season but has scored 103 goals for the club.
Their match at Stamford Bridge is crucial with Utd sitting just a point below the Blues in fifth place.
