Ronaldo also missed the first leg of the round of 16 tie, with Madrid cruising to a 3-0 win at the Santiago Bernabeu without their star attacker.
He then returned to the starting XI for the 5-0 win over Granada at the weekend, but will be allowed to sit out Thursday's clash again.
Modric, meanwhile, has featured for the full 90 minutes in Madrid's first two games of 2017, but Zidane does not need the Croatia international at the Ramon Sanchez Pizjuan.
The capital side will also be without the services of James Rodriguez in this week's return. The former Monaco star netted twice in the first leg, but is unavailable due to injury.
"James felt something in his calf again and we will not take any risks," Zidane explained.
"I think it is only a small thing, but we are always careful. We still have a lot of games left to play. We will see how his situation evolves, but we will not risk him."
Isco will also miss the trip to Sevilla due to a minor problem, while Pepe and Gareth Bale remain unavailable, too.
Sergio Ramos, Lucas Vazquez and Mateo Kovacic all return.