Germany beat Costa Rica 4-2 on Friday (AEDT), but the victory at Al Bayt Stadium was not enough for it to progress from Group E due to Japan's shock win over Spain.
A topsy-turvy second half saw Germany, who had gone ahead through Serge Gnabry's early goal, fall behind before Kai Havertz grabbed a double and Niclas Fullkrug completed the scoring.
Germany finished third, condemned to a second straight group-stage exit from the World Cup, after they had progressed from the first round in each of their 16 previous such appearances at the tournament.
With Euro 2024, which Germany are hosting, on the horizon, Flick believes wholesale alterations are needed to the way football is coached in the country, with a back-to-basics approach required.
"We do have players who play at top clubs, we do have the qualities," Flick said.
"I believe that for the future of German football we need to do things differently in training. For years we talk about new goalkeepers or new wing-backs, but what was always very good in German football was that we were able to defend well.
"We need the basics. Even though Spain lost against Japan, they are very good in defence and they focus on training the youngsters to those tactics.
"For the future, even for the next 10 years, this is vital."
Musiala's performance throughout the tournament has been one bright spot to come from Germany's disappointing campaign.
The Bayern Munich youngster was superb against Costa Rica. He had eight shots, two of which hit the post while two forced Keylor Navas into smart stops. His 24 touches in the opposition box was the most recorded in a World Cup game since such records began in 1966.
Musiala represented England at youth level and came through Chelsea's academy, and when asked by Stats Perform if the 19-year-old was a player to build around heading towards Euro 2024, Flick suggested the playmaker's upbringing helped prove his point about the weaknesses in Germany's approach.
"Jamal, what he showed today, it's so unfortunate that such a player cannot continue in the tournament," Flick said.
"He's fantastic, his skills in the tackles, the one-v-ones, he's outstanding. We do have talents, it has to be said, we are headed in the right direction, but we have to focus on the training.
"Jamal has been trained in England, not in Germany. We have Kai [Havertz], and he was able to really bring his A game."
Flick feels Germany's future can be bright, though.
He said: "We can get up quickly and recover. We will see what the future looks like. See how we can implement our idea.
"We need to assess our work here, head in a different direction. This is the next step. We will do that very soon.
"I am a very critical person and we will assess everything."