"Investigators did not furnish evidence proving his guilt," the court said.
Alexander Prokofyev was accused of selling and giving his patients Ketamine, commonly known as "Special K" and generally used as a veterinary and medical anesthetic, banned for human consumption in some countries.
"For two years [of the trial] I have believed I was right," Prokofyev said. "I hoped the judge would be able to solve the case."
Prokofyev's lawyer, Yevgeny Chernousov, said acquittals were extremely rare in modern-day Russia.
"Being acquitted is tantamount to playing Russian roulette: you pull the trigger and unexpectedly stay alive," the lawyer said.
Investigators contended Prokofyev, the former director and chief physician of the Medical Services clinic, had used Ketamine in surgery without holding a relevant license and sold the substance. Investigators accused him of selling 50 ampoules, or 5 grams, of Ketamine between January 10 and June 24.
"The goals and motives behind my activities as a doctor were to help patients," Prokofyev said in court. He sought acquittal on all charges and maintained he had not sold the drug.
Prosecutors who had insisted Prokofyev should be sentenced to seven years in jail on charges of storing and selling psychotropic substances in large amounts said they would consider appealing the court ruling.