Church officials, however, cited an additional issue driving discontent: same-sex marriage, which Pena Nieto has proposed legalizing across the country and enshrining in the constitution. Some senior officials in the church even claimed credit for fomenting a punishment vote, saying the Catholics cost Pena Nieto and his party at the polls.
"I think this failure of the PRI (the governing party) on the national level also has to do with this initiative," said Bishop Luis Gallardo Martin del Campo of Veracruz.
"It will make the president see that he cannot impose it on the majority of the population," Bishop Gallardo added June 7 in remarks that received national coverage.
How much the same-sex marriage issue and Catholic Church intervention -- along with the intervention from evangelical congregations -- swayed Mexico's recent elections remains disputed.
Mexican society has not traditionally mobilized over controversial social issues such as same-sex marriage and abortion, even though polling shows opposition to the issues and census data say 83 percent of the population professes Catholicism. A poll in the newspaper El Universal published after the elections showed 49 percent of Mexicans opposed same-sex marriage, though 43 percent approved. Nearly 70 percent disagreed with same-sex couples adopting children.
Some church observers say the bishops are overstating their influence, which they say carries more currency in elite circles and polite society than with the masses. A spokesman for the Mexican bishops' conference was unavailable by deadline.
"The Catholic Church historically has had as a practice forming direct links with elites and the political class, but distanced itself for much of that time from the citizenry and the faithful," said Bernardo Barranco, a columnist and church observer.
He points to the church's unsuccessful call to avoid voting for the Party of the Democratic Revolution over its decriminalization of abortion and approval of same-sex marriage in Mexico City. Barranco also asked if social issues were so important to voters, how the president's party won convincingly in several states, such as Sinaloa and Zacatecas in northwestern Mexico, while suffering defeats in states with similar Catholic populations, such as Chihuahua on the U.S. border.
"The hierarchy does not have the ability to decide for the masses, at least for the issues such as gay marriages," Barranco said.
In May, Pena Nieto proposed recognizing same-sex marriages in all of Mexico's states, along with allowing gay couples to adopt children. School textbooks would also be changed to reflect diversity, he said.
The proposal followed Mexican court rulings that established jurisprudence on the issue and said state laws limiting marriage to only members of the opposite sex were discriminatory. Same-sex couples can currently marry in some states, though anyone in practice can marry by obtaining a court injunction.
Pena Nieto's proposal, which Catholic officials said they were not advised of, drew a muted church reaction initially, though in the conservative state of Aguascalientes, Bishop Jose de la Torre Martin issued a letter urging locals to vote in favor of the family.
"This defends life, this defends the family, this defends the rights of parents to educate," El Universal reported the bishop saying of the pro-family vote.
Attempts to reach a diocesan spokesman were unsuccessful.
A source involved with one of the political parties, who was unable to speak for attribution, said pre-campaign polling in Aguascalientes found residents concerned with local issues such as water, public transportation and security, while not mentioning same-sex marriages. Others suspected social issues emerged as election day neared.
"Social conservatism definitely played a role," said Andrew Paxman, history professor at the Center for Research and Teaching in Economics in Aguascalientes, "not only with the bishop's pastoral letter, but more so because of the perceived liberalism of the PRI in general, especially with its federal gay-rights agenda."
Members of Pena Nieto's own party also questioned if the president's proposal had cost them votes.
Ex-presidential candidate Francisco Labastida Ochoa told Radio Formula he had seen polls putting Institutional Revolutionary Party candidates ahead prior to the president's proposal -- only to drop in the final three weeks of campaigning.
The explanation caused some disbelief from critics, who wondered if the party was inventing excuses instead of recognizing citizen complaints such as corruption.
"It's not the errors of the PRI or the robberies by the (governor of Veracruz) or the killing of journalists or the bad economy. Gays are to blame," tweeted Rodolfo Soriano Nunez, a sociologist who studies the church. He said the electoral response showed the church focusing more on hot-button social issues instead of matters like crime and corruption, which drove voter discontent.
The conflict over same-sex marriage appeared to signal a shift in church-state relations, which were considered close under Pena Nieto -- so close he was taken in 2009 to the Vatican, where he made his wedding plans public for the first time in an audience with then-Pope Benedict XVI. The bishops' postelection pronouncements, however, put them on a confrontational path with Pena Nieto -- rare in Mexico, where prelates also tend not to openly criticize the president or local elites.
"The church lent Pena Nieto a lot of legitimacy," said Ilan Semo, political historian at the Jesuit-run Iberoamerican University, "but something broke between them, something profound."
Father Hugo Valdemar Romero, spokesman for the Archdiocese of Mexico City, called the change in presidential posture "a betrayal."
Father Valdemar said the issue will "play out in the next election," with lay Catholics taking the lead because prelates' political pronouncements are limited by the law.
Other observers, however, see social trends moving in the opposite direction. A Pew Research Poll shows 61 percent of the Mexicans answering yes to the question: "Should society accept homosexuality?"
"The Church in Mexico might be able to delay it, but gay marriage in Mexico is an inevitability," said Andrew Chesnut, a religious studies professor at Virginia Commonwealth University. "Mexicans accept homosexuality at the same rate as people in U.S. and Brazil," where same-sex marriage has become legal.