Germany, who host the Euros next year, have been struggling for form and have won just one of their last five matches since their shock World Cup group stage exit in December.
The four-time world and three-time European champions, who have now been eliminated in the first round of the last two World Cups, have also won only three of their last 11 games.
Flick did not include RB Leipzig striker Werner or Bayern Munich midfielder Goretzka, who has 53 caps, in his squad, with David Raum and Thilo Kehrer also notable absentees.
Bayer Leverkusen defender Jonathan Tah returned to the squad following a strong campaign last season, while the speedy Robin Gosens, who is enjoying his Bundesliga start with Union Berlin, was also recalled.
A surprise inclusion is Brighton & Hove Albion forward Pascal Gross, who is waiting for his first cap.
The Germans host Japan in Wolfsburg on September 9 before taking on France in Dortmund three days later.
With Germany fans booing and jeering in their matches in June, Flick is under mounting pressure with the upcoming games likely his last chance to show clear improvement towards a battle-worthy team for next year's tournament.
