The substitution caught Marcelo off guard at Montivili as he told reporters post-match: "I was surprised by the substitution but I respect the decision of the coach, I wanted to continue because I felt 100 per cent.
"We are on the right road and I am sure we are going to improve with each game. We played well today and we got the three points."
Lopetegui was also asked about the substitution during his news conference and the former Spain boss said: "We wanted to tighten things up down that side and focus on being good in the air, an area the opposition are very good in."
Borja Garcia gave Girona a surprise 16th-minute lead before Madrid captain Sergio Ramos equalised from the penalty spot 23 minutes later.
A Karim Benzema brace and Gareth Bale's goal then completed Madrid's comeback away from home.
"We're satisfied with the win because they're three very important points away from home," Benzema said. "We'll look to continue on in the same vein. We're keen to perform well in LaLiga this season.
"I've been here for 10 years and always work hard for the team. I'm raring to score a lot of goals and help the team to pick up silverware. Football isn't all about goals, it's about winning games and playing well. I'll be trying to score a lot of goals to help the team."
In-form Wales forward Bale added: "Starting well is key in LaLiga and we are happy with the win over Girona. We know the game lasts 90 minutes, not 45, and we have to take our chances. That’s football.
"I am ready to help the team, we are united, we work well together and want to win every trophy possible. I’d like to take penalties, but the coach decides, and I have to respect his decisions."