City could not include more than 17 overseas players in their squad.
And Guardiola still has 18 on his books, despite letting four foreign internationals leave before Wednesday's transfer deadline.
Clubs can change three players after the group stage but Toure, 33, will not be able to play against Borussia Monchengladbach, Celtic and Barcelona.
The Ivory Coast international has played a major part in all City's trophy wins since he was bought from Barcelona, then managed by Guardiola, for £24m in 2010.
