Midfielder Kroos, who has just signed a new Real Madrid contract keeping him at the club until 2023, and Barcelona goalkeeper Ter Stegen sit out the qualifiers, away to Belarus on June 8 and then home to Estonia three days later in Mainz, with leg injuries.
Germany are unbeaten in Group C and sit second behind leaders Northern Ireland after a 3-2 away win in their opening game against the Netherlands in March.
Captain Manuel Neuer has been included "for now", say the German Football Association (DFB), but the Bayern Munich goalkeeper has been carrying a calf injury and missed the last five games of the German league season.
The Bavarians are hoping Neuer can play in the German Cup final in Berlin on Saturday against RB Leipzig with the newly-crowned Bundesliga champions hoping to clinch the domestic double.
Germany's 22-man squad for Euro 2020 qualifiers against Belarus and Estonia in June:
Goalkeepers: Manuel Neuer (Bayern Munich), Bernd Leno (Arsenal/ENG), Kevin Trapp (Eintracht Frankfurt)
Defenders: Matthias Ginter (Borussia Moenchengladbach), Marcel Halstenberg (RB Leipzig), Jonas Hector (Cologne), Thilo Kehrer (Paris SG/FRA), Lukas Klostermann (RB Leipzig), Nico Schulz (Hoffenheim), Niklas Stark (Hertha Berlin), Niklas Suele (Bayern Munich), Jonathan Tah (Bayer Leverkusen)
Midfielders: Julian Brandt (Bayer Leverkusen), Julian Draxler (Paris SG/FRA), Serge Gnabry (Bayern Munich), Leon Goretzka (Bayern Munich), Ilkay Gundogan (Manchester City/ENG), Kai Havertz (Bayer Leverkusen), Joshua Kimmich (Bayern Munich), Marco Reus (Borussia Dortmund), Leroy Sane (Manchester City/ENG)
Forward: Timo Werner (RB Leipzig)