Fitness problems meant both players missed France's opening qualifying matches in March, when they beat the Netherlands 4-0 at home and won 1-0 away to the Republic of Ireland.
They now go into a match against minnows Gibraltar in Faro and a home clash with Greece, on top of qualifying Group B with six points.
"You will say I am very pragmatic, but the three points that are available against Gibraltar have the same value as those we took against the Netherlands or in Ireland," Deschamps told reporters in Paris.
"He was supposed to be in the squad for the World Cup but was ruled out by injury, but now he is back on top form," added Deschamps of Nkunku, who scored four goals in the last five Bundesliga games of the season for his club as they finished third.
He is set to feature for Leipzig in this weekend's German Cup final against Eintracht Frankfurt.
Chelsea centre-back Wesley Fofana is also in the squad and will hope to make his full France debut after withdrawing from the March list due to injury.
Real Madrid left-back Ferland Mendy was also handed a first call-up since before the World Cup, while injured Arsenal defender William Saliba is among the notable absentees.
Highly-rated Nice midfielder Khephren Thuram was left out, while Juventus midfielder Paul Pogba and Chelsea's N'Golo Kante - two stars of France's triumphant 2018 World Cup campaign - are again absent after injury-ravaged seasons.
France squad:
Goalkeepers: Alphonse Areola (West Ham United/ENG), Mike Maignan (AC Milan/ITA), Brice Samba (Lens)
Defenders: Axel Disasi (Monaco), Wesley Fofana (Chelsea/ENG), Theo Hernandez (AC Milan/ITA), Ibrahima Konate (Liverpool/ENG), Jules Kounde (Barcelona/ESP), Ferland Mendy (Real Madrid/ESP), Benjamin Pavard (Bayern Munich/GER), Dayot Upamecano (Bayern Munich/GER)
Midfielders: Eduardo Camavinga (Real Madrid/ESP), Youssouf Fofana (Monaco), Antoine Griezmann (Atletico Madrid/ESP), Adrien Rabiot (Juventus/ITA), Aurelien Tchouameni (Real Madrid/ESP)
Forwards: Kingsley Coman (Bayern Munich/GER), Ousmane Dembele (Barcelona/ESP), Olivier Giroud (AC Milan/ITA), Randal Kolo Muani (Eintracht Frankfurt/GER), Kylian Mbappe (Paris Saint-Germain), Christopher Nkunku (RB Leipzig/GER), Marcus Thuram (Borussia Moenchengladbach/GER)
