Sergio Aguayo, a political analyst at the elite Colegio de Mexico, said Gordillo "wasn't just a shadow power, but one that wanted to be a political power."
"In Pena Nieto's vision of Mexico, no one can be above the president," Aguayo said. "It's the same old imperial presidency."
Gordillo's combativeness may have led her to miscalculate Pena Nieto's willingness to reinstate the old tradition of unquestioned presidential authority.
"She underestimated him," columnist and political analyst Raymundo Riva Palacio said of Pena Nieto.
The PRI, which ruled Mexico from 1929 to 2000, spent 12 years out of power before returning to the presidency with Pena Nieto's 2012 election victory.
Gordillo's arrest recalled the 1989 detention of once-feared oil union boss Joaquin Hernandez Galicia. He had criticized the presidential candidacy of Carlos Salinas and threatened a strike if Salinas privatized any part of the government oil monopoly.
On Jan. 10, 1989, about a month after Salinas took office, soldiers used a bazooka to blow down the door of Hernandez's home in the Gulf Coast city of Ciudad Madero.
He was freed from prison after Salinas left office.
Salinas' sweep of old, uncooperative union bosses also led to opening the way for a new, up-and-coming leader in the teachers union, Gordillo, who was at first seen as a reformer.
Gordillo's arrest alone is far from enough to help Pena Nieto improve Mexico's schools. So great is the union's control over hiring that even the government acknowledges it's not sure how many schools, teachers or students exist in Mexico.
The Mexican education system has been persistently one of the worst performers among the world's developed economies, with few signs of improvement. Nearly every Mexican 4-year-old is in pre-school, but only 47 percent are expected to graduate high school. In the U.S., the number is closer to 80 percent.