Raul Albiol is on hand to partner Raphael Varane if Portugal's Pepe fails to recover from injury with fellow centre-back Sergio Ramos suspended.
"Pepe suffered a muscle injury during the Levante game and we will know tomorrow for sure if he will be on the pitch or not," Mourinho told a news conference in Istanbul on Monday.
"But my team is made up of good players and Albiol will play in his position if Pepe can't. I am confident that all players in my squad are capable."
Real romped to a 5-1 victory at home to mid-table Levante in La Liga on Saturday as Mourinho left several top performers, including forward Cristiano Ronaldo, out of his starting lineup. Ronaldo still scored as a substitute.
Despite their good form and healthy first-leg lead, Mourinho has cautioned his players against complacency.
"There have been examples of teams losing the second leg 3-0 after a 3-0 victory in the first game so I warned my players to be careful... to avoid any unpleasant outcomes," Mourinho said.
"During the meeting today we also discussed different attacking tactics as Galatasaray had switched from a four-man defence to three in the first game."
Galatasaray and their forward Didier Drogba, who won the trophy last season with Chelsea and enjoyed some of his best years when Mourinho coached the London club, face a tough ask but at least have a famously fervent crowd to count on.
Mourinho said his players were looking forward to playing in front of "50,000 passionate fans" in Istanbul.
"I won't go home happy if we lose tomorrow. Even if we get a result to qualify through losing, that won't make me happy. We came here with only one thing in mind and that is to win," he said.
