Netherlands coach Bert van Marwijk, who named his 23-man squad on Friday, replaced the injured duo with Jeremain Lens and Georginio Wijnaldum
Robben has an inflammation affecting the groin and will not be available for Bayern Munich this weekend but Van Marwijk said: "I am keeping the door open for him if his injury improves next week."
Barcelona midfielder Afellay is still recovering from a muscle injury.
Netherlands had their last friendly match against Englan called off due to the riots in London earlier this month, but have still overtaken world champions Spain at the top of the FIFA rankings.
"Normally I'm not interested in stats like that but this is different," said Van Marwijk.
"This is based on our results the last four years and then it says something about what we are doing and that makes me proud."
Netherlands are top of Group E with 18 points after six matches, three more than Sweden, who will be their opponents in the final qualifying match on October 11.
Squad:
Goalkeepers: Maarten Stekelenburg (AS Roma), Michel Vorm (Swansea City), Tim Krul (Newcastle United)
Defenders: Khalid Boulahrouz (VfB Stuttgart), Edson Braafheid (Hoffenheim), Jeffrey Bruma (SV Hamburg), John Heitinga (Everton), Hedwiges Maduro (Valencia), Joris Mathijsen (Malaga), Erik Pieters (PSV Eindhoven), Gregory van der Wiel (Ajax Amsterdam).
Midfielders: Mark van Bommel (Milan), Nigel de Jong (Manchester City), Wesley Sneijder (Internazionale), Kevin Strootman (PSV Eindhoven), Rafael van der Vaart (Tottenham Hotspur), Georginio Wijnaldum (PSV Eindhoven)
Forwards: Eljero Elia (SV Hamburg), Klaas Jan Huntelaar (Schalke 04), Luuk de Jong (Twente Enschede), Dirk Kuyt (Liverpool), Robin van Persie (Arsenal), Jeremain Lens (PSV Eindhoven).
