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.
“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 £14m 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.
Hamilton midfielder Simon Mensing recently served a four-week ban after he tested positive for a specified substance.
The 28-year-old Mensing tested positive for the stimulant methylhexaneamine at the end of January and subsequently missed five matches after a period of ineligibility was imposed on him.
The player maintained he was unaware he had ingested the substance while using a dietary supplement – an explanation which was accepted by UK Anti-Doping.
The FA last night released a short statement, saying: “The FA can confirm that a player has been provisionally suspended from playing pending investigation, having tested positive for the use of a prohibited substance.”
It is understood that Toure was not included in City’s squad for Wednesday night’s FA Cup match against Aston Villa because the club were aware of the situation.
The failed test automatically triggered the suspension, with City left with no option but to exclude him from their plans until the conclusion of proceedings.
QPR goalkeeper Paddy Kenny received a nine-month ban during his time at Sheffield United after testing positive for specified substance ephedrine.