People called the police when saw the man touching the boy's face, legs and genitals.
The four Díaz sisters and some male relatives played the instrument while people took communion.
About 100,000 gathered on the dirt field of a sports complex for the Mass in San Cristóbal de las Casas.
The visit, at the midway mark of Pope Francis' five-day trip to Mexico, is also aimed at boosting the faith in the least Catholic state in Mexico.
Subraya importancia del decreto que permite el náhuatl como lengua litúrgica
Francis' visit comes amid strong challenges to the church in the southern state of Chiapas.
El Papa entregará un decreto de autorización de uso de lenguas indígenas en la liturgia católica, misas y otras ceremonias, durante su visita a Chiapas
El jerarca católico presentará el decreto el 15 de febrero en su misa en Chiapas
The four Díaz sisters began playing marimba in churches three decades ago at the invitation of the late Chiapas Bishop Samuel Ruiz.
Dos trabajadores cayeron de un andamio desde una altura de 15 metros y se reportan en estado grave; los trabajos formaban parte de los preparativos ante la visita del papa