"Phil is a very important player and we have to remember that he was out for a long time," Martinez told reporters on Tuesday.
"It's a real opportunity for us to have Phil Jagielka refreshed and fully fit going into tomorrow's game."
Everton, 12th in the table, have conceded 34 goals in 23 Premier League games this season, and both keeper Tim Howard and young central defender John Stones have come under scrutiny.
Martinez confirmed Howard would not feature, with Joel Robles, who has been in goal for all of Everton's cup fixtures this season, keeping his place against City.
The manager also offered a robust defence of Stones, saying he had the potential to become an all-time great for his country.
"John is 21. He has incredible potential but he is still a young man," Martinez said.
"Whatever the judgement from the outside, we accept it, that is part of the game, but I think Stones is in the right pace to fulfil his potential and become one of the greatest players England has ever seen."
Everton travel to the Etihad Stadium with a 2-1 advantage from the first leg, and Martinez is hoping that getting to the final at Wembley will help alleviate fans' disappointment with their league position.
"Man City have one of the best home records and we know it is a massive challenge, but we want to be successful and we will give everything we've got to try and make the final," he said.
(Reporting by Simon Jennings in Bengaluru; Editing by Mark Potter)
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