Loftus-Cheek opened the scoring in the second leg of the Europa League semi-final meeting with the Bundesliga outfit but with the game heading towards extra-time was replaced by Ross Barkley in the 86th minute.
The decision was met with boos from a number of Blues supporters in what was the latest in a number of strong fan reactions to Sarri's decisions throughout his first season in charge.
The former Napoli boss was vindicated in the end, with Barkley scoring his penalty during the 4-3 shootout win that sends Chelsea to the final to face London rivals Arsenal.
And Loftus-Cheek hit out at those who questioned Sarri, claiming that his own struggles with fitness in recent months meant taking him off was the right thing to do.
"I've played a lot in these last few weeks, more than I've done in my career. So I think I have to pay attention to my body and take care of myself because I don't want another injury," Loftus-Cheek told reporters.
"When I feel that I'm a liability to the team, because I was getting cramp in my hamstrings just before I came off, and the minute I feel if I sprint it could go or I won't be able to spring as fast as I can, then it's just the right decision to put some fresh legs on.
"The fans didn't like it but I tried to lift them because we didn't need that atmosphere here. But it's all for a good reason. Gianfranco [Zola] asked me five minutes before and I said I was good.
"But then I felt the cramp on a sprint and thought 'let's not risk it'. Obviously, Ross coming on and putting that penalty away - it's all that matters."
Loftus-Cheek's first-half strike was his 10th goal of the campaign in all competitons despite having only made 16 starts since returning from a successful loan spell at Crystal Palace last term.
He has forced himself into Sarri's first team in recent weeks, however, having seemingly overtaken Barkley and Mateo Kovacic in the midfield pecking order to start alongside mainstays N'Golo Kante and Jorginho.
And while the 23-year-old already possesses a Premier League winner's medal for his bit-part role in Antonio Conte's side's title win in 2016-17, the Europa League final signifies the first time for the Chelsea academy product to properly contribute to winning some silverware for the club.
Unsurprisingly, Loftus-Cheek sees the clash in Baku on May 29 as the biggest match of his career to date.
"It feels amazing to be in a European final," he added. "This is why we love football; it's amazing. I was so nervous on the sideline. But it just felt amazing when Eden [Hazard] put that last penalty away, knowing we're going to Baku for the final.
"I've been watching the [Champions League] games and I couldn't believe it. It's great for English football. It would feel amazing to be a main player in the team, with goals and assists, to then lift that trophy. I don't know what that feeling would be like as I've never done it. But it would be amazing.
"So we're looking forward to it. It will be a tough one. Firstly, it will just be amazing to be a part of a European final. It will be the biggest game of my career if I do play. But I look forward to it with all the excitement and fun that comes with it.
"And I think we have to do that, you know, coming into a big game like that we've got to be focused but also enjoy it. It's such a big occasion that sometimes you can let it get to you but I think we just have to be relaxed and enjoy it and play our best football. Against Arsenal, another English side will be fun."
Before that meeting the Blues will round out their Premier League campaign on Sunday when they travel to the King Power Stadium to take on Leicester City.