The club confirmed in a short statement on their website that Toure had been informed by the Football Association that an A-sample provided by him returned positive.
"He has been suspended from participating in all first team and non-first team matches pending the outcome of the legal process," the City statement read.
It added: "There will be no further comment from the football club at this stage."
The World Anti-Doping Agency define a specified substance as one that is "more susceptible to a credible, non-doping explanation".
The WADA punishment for such a positive test ranges from a warning to a two-year ban.
The 29-year-old centre-back joined City for ?£14million in 2009, ending a seven-year association with Arsenal.
Gunners boss Arsene Wenger had signed him from Ivorian side Mimosas and he went on to captain the club on a number of occasions before heading to Eastlands, where he served as club captain under Mark Hughes until he was succeeded by Carlos Tevez for this season.