The cleric, whose tacit support of the human-rights demands espoused by Zapatista rebels has antagonised critics,has reached the retirement age for priests after 40 years' service. Parishioners queued for hours for the Mass which juxtaposed Gregorian chants and marimba tunes with prayers in Tztotzil and Tzeltal, local Indian languages.
Bishop Ruiz told the congregation he was not about to go gently. In deference to the Holy See, he had already penned his anticipated resignation letter but vowed to the packed pews on Wednesday that "I will not sign it until just before the stroke of midnight". "Viva Don Samuel!" roared the throng that spilt out of the cathedral to fill the plaza.
As one of the last senior practitioners of liberation theology in the Latin American church, he resisted being sidelined by the Pope, despite his politics, and was twice nominated for the Nobel Peace Prize. When the papal nuncio to Mexico attempted to nudge the bishop aside in 1993, 20,000 Maya Indians converged on the cathedral to support the man they call "Tatik"- father.
Bishop Ruiz is expected to keep his position until the Pope approves his offer to quit, probably not before 25 January, when he will have completed four decades in the diocese.
Lately, an uneasy peace has settled on Chiapas, one of Mexico's poorest and most isolated states, which shares a frontier with Guatemala and has provided refuge to generations of refugees.
For now, army patrols and paramilitary groups are maintaining a lower profile during primary election campaigns. The guerrilla leader Subcomandante Marcos unleashes rhetoric on the Internet rather than volleys of bullets.
In January 1994, when the Zapatistas emerged and fired shots from the town hall balcony adjacent to the cathedral, Bishop Ruiz was hounded for not condemning them unconditionally and for echoing some of their demands for justice. Anti-communists accused him of blessing the weapons of the National Zapatista Liberation Army, even though he never condoned their violence. President Ernesto Zedillo accused him of preaching a "theology of violence'' and siding with the Zapatistas.
Bishop Ruiz tried to negotiate a peace between the state and the guerrillas. After assassins fired on his car he wore a bullet-proof helmet whenever he trekked through the bush to visit Indian communities.
Almost a third of San Cristobal's population of 190,000 are Mayan. Under Bishop Ruiz, say supporters, "these Indians dare to raise their eyes. He has shown them their human dignity." Only 60 per cent are Roman Catholic, now that the rest have converted to evangelical sects. Divisions are rife in this Spanish colonial town and its outlying villages.
Ethnic groups frequently feud, indigenous Catholics target evangelical Christians, cliques within religious denominations squabble, political parties back-stab, landowners hire paramilitaries to intimidate outsiders and nearly 150 non-government organisations vie to pick up the pieces.
Mariano Diaz Ochoa, the mayor, an ex-businessman loyal to Mr Zedillo's ruling Institutional Revolutionary Party, spoke candidly about Bishop Ruiz's retirement. "His leaving will contribute to the achievement of peace in Chiapas. He is more dedicated to politics than to the church and so we felt a bit deceived. We don't really know him in town. He worked more with outlying indigenous communities."
Indeed, Bishop Ruiz boasts that the church in Chiapas "penetrates to places that the state doesn't." He arrived in 1960 as a conservative, but soon innovated programmes that tackled repression, illiteracy, malnourishment, and disease. Spanish was not widely understood in remote hamlets, so he organised a network of lay instructors to teach the gospel in local dialects.
In 1988 Bishop Ruiz founded the Fra Bartolome Centre for Human Rights, in honour of the town's namesake, Bishop Bartolome de las Casas, who protected the Indians from exploitation as slaves in colonial times. The director of the institute, Marina Jimenez Ramirez, said: "Bishop Las Casas felt indignation. But Bishop Ruiz makes this indignation contagious and won't stand for pain and suffering ... He's always tried to keep the authorities in check, whether army, police, or politicians. He works with the people."
Defamation, death threats, an attack with a hammer on his sister while she stirred a pot on the parish stove - nothing has silenced Bishop Samuel Ruiz.
In 1995 the Vatican sent out Raul Vera to act as an auxiliary bishop in the hope of curbing some of Bishop Ruiz's revolutionary zeal but the new number two backed up almost all the bishop's positions. "The Vatican took the decision that there were doctrinal errors but they didn't count on the reaction of the people," Bishop Vera said. "In this Don Samuel is a realist. He has no illusions in his fight for justice."
Speculation about his successor dismisses the possibility of Bishop Vera taking charge. Most of Bishop Ruiz's enemies would prefer to replace him with someone much closer to the establishment.
Jorge Santiago, a writer jailed without charge in 1995 for two months on suspicion of being the liaison between the Zapatistas and the bishop, says: "Don Samuel cannot be neutral. His revolution ... is not obstructed even by a deeply conflicted Chiapas. In his way the bishop is much more subversive than Marcos, because he transforms society through faith."