Otomi Indians Alberta Alcantara Juan and Teresa Gonzalez Cornelio have spent almost four years in prison on 21-year sentences for the alleged kidnapping of six federal agents.
Prosecutors say the agents were confiscating pirated good at a market in 2006 when angry vendors overpowered them and held them against their will.
The court ruled Wednesday there was insufficient evidence to convict the women. Critics, including Amnesty International, contend prosecutors fabricated evidence.
A third woman convicted in the case, Jacinta Francisco Marcial, was freed last year.