Both players picked up groin injuries in the 3-2 win over Hertha Berlin which stretched their unbeaten league run to 35 matches and were initially confident of recovering in time for the match.
"They are not yet fit but that is not a problem," Guardiola, who said Kroos was in better condition than Robben, told reporters.
The Spaniard does expect them to be back in action in the Champions League next week at Viktoria Plzen.
He will have central defender Dante back, after he recovered from a cut in his leg that ruled him out for two weeks.
"Dante has been training well and things are looking very, very good," Guardiola said.
Treble winners Bayern lead the Bundesliga with 26 points from 10 games, one ahead of Borussia Dortmund and Bayer Leverkusen.
Their last league defeat was in October 2012 when they lost 2-1 to Leverkusen. Hamburg SV hold the longest unbeaten run with 36 games set 30 years ago in 1982-83.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
Share
