Juventus centre-back De Ligt missed Wednesday's Champions League win at Lokomotiv Moscow with an ankle injury, while Depay will sit out Lyon's Ligue 1 game against rivals Marseille this weekend with a thigh problem.
But Donyell Malen, who has scored 16 goals for PSV Eindhoven this season, does miss out through injury.
Koeman has handed maiden call-ups to AZ Alkmaar youngsters Myron Boadu and Calvin Stengs.
The Dutch, who lead qualifying Group C ahead of Germany on head-to-head record, can secure a Euro 2020 finals spot by avoiding defeat against Northern Ireland in Belfast on November 16, before facing Estonia three days later.
The Netherlands are bidding to qualify for a major tournament for the first time since finishing third at the 2014 World Cup.
Goalkeepers: Jasper Cillessen (Valencia/ESP), Kenneth Vermeer (Feyenoord), Jeroen Zoet (PSV Eindhoven)
Defenders: Patrick van Aanholt (Crystal Palace/ENG), Nathan Ake (Bournemouth/ENG), Daley Blind (Ajax), Virgil van Dijk (Liverpool/ENG), Denzel Dumfries (PSV), Matthijs de Ligt (Juventus/ITA), Joel Veltman (Ajax), Stefan de Vrij (Inter Milan/ITA)
Midfielders: Donny van de Beek (Ajax), Frenkie de Jong (Barcelona/ESP), Davy Propper (Brighton/ENG), Marten de Roon (Atalanta/ITA), Kevin Strootman (Marseille/FRA), Georginio Wijnaldum (Liverpool/ENG)
Forwards: Ryan Babel (Galatasaray/TUR), Steven Berghuis (Feyenoord Rotterdam), Myron Boadu (AZ Alkmaar), Luuk de Jong (Sevilla/ESP), Memphis Depay (Lyon/FRA), Quincy Promes (Ajax), Calvin Stengs (AZ), Wout Weghorst (Wolfsburg)