The cathedral was closed after dozens of supporters of former leftist presidential candidate Andres Manuel Lopez Obrador stormed the building bordering the capital's central square on Sunday, scuffling with faithful and overturning pews, according to a statement posted on the church's Web site.
The Archdiocese of Mexico described the incident - which delayed Sunday Mass, frightened some parishioners out of the building and forced priests to take refuge in the sacristy - as an act of violence against the church.
One elderly parishioner was slightly injured in the scuffle, according to Father Ruben Avila, who is in charge of the Cathedral.
"Of all sudden, the whole cathedral shook with their shouting, and they pushed the parishioners within a few meters (yards) from the door of the sacristy," Avila said in an article posted on the Archdiocese's Web site.
The protesters shouted slogans against Cardinal Norberto Rivera, who they claim has become involved in politics, something clerics are forbidden to do by Mexican law. Avila estimated the number of protesters at 150.
Mexican news media said the protesters complained that the church rang its bells for an unusually long time, disrupting a Lopez Obrador rally in the plaza known as the Zocalo.
Lopez Obrador's followers several times have interrupted services at the cathedral, chanting slogans against electoral fraud they believe cost their candidate the July 2006 presidential elections.
Since that loss, Lopez Obrador has declared a government-in-resistance and encouraged followers not to recognize President Felipe Calderon. Electoral officials upheld Calderon's slim victory after more than two months of investigating allegations of fraud.
At the Sunday rally of under 100,000 - the smallest crowd Lopez Obrador has drawn in a series of mass meetings in the Zocalo since 2006 - he called on Mexico's government to invest US$36 billion (€24.6 billion) to combat oil declining reserves.
He also asked his followers to resist any possible privatization of the oil industry.
"We are facing one of the nation's most critical moments," Lopez Obrador said, referring to declining oil production and the lack of refinery capacity at the state-run oil company Pemex that forces the country to import gasoline.