Ronaldo was taken off as a precaution at halftime during the 1-1 draw in the first leg at the Bernabeu on Tuesday suffering with a hamstring strain.
Although coach Carlo Ancelotti played down the injury and said he was fit to face Atletico, the Portugal forward has not been risked from the start at the Calderon.
Argentina winger Di Maria, who finished the season in blistering form and has looked strong in pre-season, has turned down a new deal at the Bernabeu and has been linked with a move to the English Premier League.
"Di Maria asked to leave this summer and rejected the option to renew," Ancelotti told a news conference on Thursday. "We'll look for the best option for him and if at the end of August he is still here then he will work with us like last season."
Germany midfielder Sami Khedira's days also appear numbered at Real after he was left out for the second successive game.
"He has a year left on his contract and has rejected a new deal. It is a different situation to Di Maria because he hasn't asked to leave," added Ancelotti.