Long-term injury casualty Luca Zidane also missed the session but Gareth Bale and co returned following their successful participation in the Fifa Club World Cup.
Real beat Al Jazira 2-1 in the Wednesday's semi-final before capturing their fifth Club World title with a 1-0 victory over Gremio in the final played on Saturday (17 December) at the Zayed Sports City Stadium in Abu Dhabi.
Ronaldo scored the winner and played the full 90 minutes during the final against the Brazilian side but the five-time Ballon d'Or winner was a surprising absentee from the workout when the rest of his available teammates returned to training to prepare for the El Clasico against Barcelona.
Karim Benzema was also missing but played 80 minutes of the final at the Sheikh Zayed Stadium before being replaced by Bale. Real have not disclosed the reason behind the absentees from but Zidane will be hoping both forwards will be fully fit for Barcelona's visit to the Bernabeu.
Barring any fresh injuries, the French boss is expected to deploy a similar line-up to the one who beat Gremio on Saturday [16 December], with Ronaldo and his compatriot leading the attack alongside Isco.
"The World champions have returned to training at Real Madrid City. After winning the Club World Cup in Abu Dhabi, the Whites now turn their attentions to the game against Barcelona on Saturday (1:00PM CET). The team will look to round off an unforgettable 2017 by winning el Clásico in LaLiga at the Santiago Bernabéu," Real Madrid informed in the club website.
"Ball work was the main focus, as the team were joined by Under-19s goalkeeper Moha, and they carried out an intense warm up before being split into two teams to work on possession and pressing. After that, they played matches on reduced size pitches. Cristiano Ronaldo and Benzema trained using the indoor facilities, whilst Luca trained along out on the pitch as part of his recovery process."
Real have a game in hand following the Club World Cup but need a victory in El Clasico to keep alive their hopes to retaining their La Liga title, with 11 points separating them from the Catalans following a disappointing start to the campaign.
Luka Modric hopes that the Club World Cup victory could serve as a motivation for the visit of Barcelona.
"We are in good shape and happy that we have this great game to play in before Christmas. We are ready and willing to give our all in el Clásico. Hopefully we will win and get closer to the top of the table," Modric said.
"Winning will depend on playing together, on how we read the game and how we play as a unified team. It is important to be together and not give Barcelona any space because if you let them play, they have players who can really punish you. The two teams have some great players and any of them can decide the game."