Wenger, who brought Toure to Arsenal in 2002, claimed that the Ivory Coast international had taken the pill after struggling with weight problems.
Toure was suspended by City on Thursday after testing positive for a "specified substance", and faces a range of punishments from a warning to a two-year ban.
Wenger said: "He wants to control his weight a little bit because that's where he has some problems and he took the product of his wife.
"It is a complete surprise because I had Kolo here for years. Very honest living, clean life, always at home - a family man. I do not suspect him at all to have taken drugs to enhance his performances.
"He was not cautious enough. I do not think there was a desire there to do something wrong and then hide it."
A "specified substance" is, as the World Anti-Doping Agency defines it, one that is "more susceptible to a credible, non-doping explanation".
Earlier this week, UK Anti-Doping revealed that Hamilton midfielder Simon Mensing had served a month-long suspension after failing a drugs test in seemingly similar circumstances. The 28-year-old tested positive for the stimulant methylhexaneamine, which was present in a dietary supplement.
Toure joined City in a £14 million deal from Arsenal in 2009 and served as the club's captain until Carlos Tevez took over last summer.