Prosecutors accused Ponosov of installing pirated Microsoft programs on the school's computers.
The court ruled the case "insignificant" and dismissed it.
Ponosov could have faced five years in prison if convicted.
He became a national celebrity due to the case.
Both Russian President Vladimir Putin and former Soviet President Mikhail Gorbachev have spoken out in Ponosov's defense.
Russia is under pressure to stop widespread music, video, and software piracy as it seeks to join the World Trade Organization.
(Interfax, ITAR-TASS, AP, Reuters)