Zavala was appointed auxiliary bishop of the Archdiocese of Los Angeles on February 8, 1994 and received his episcopal consecration from Cardinal Roger Mahony on March 19 of that year. He served as the auxiliary bishop and episcopal vicar of the San Gabriel Pastoral Region until his retirement. Bishop Zavala promoted restorative justice, opposed the death penalty, supported young people, and was a long-time supporter of immigration reform,. Although he was sometimes considered orthodox in his beliefs, he had a long history of supporting controversial positions on homosexuality.
Zavala was involved with a number of organizations: he was the bishop president of the U.S. section of Pax Christi, the international Catholic peace movement; the Co-President of Interfaith Worker Justice, an organization committed to educating, mobilizing, and organizing the religious community to advocate for better wages and working conditions for low-wage workers; and served as the Episcopal advisor to the International Commission of Catholic Prison Pastoral Care (ICCPPC). Also, he was an adjunct professor of Canon Law and Pastoral Theology in the graduate programs of Theology and Pastoral Theology at Loyola Marymount University in Los Angeles.
On January 4, 2012, Los Angeles archbishop José Gómez announced that the Vatican had accepted Zavala's resignation following the disclosure that Zavala is the father of two teenaged children. The pope accepted the resignation under Code of Canon Law c. 401 §2. In his announcement, Archbishop Gómez stated that Zavala disclosed the matter to him in early December 2011, that he had not been in ministry since, and that Zavala "will be living privately". Gómez went on to state that the children – who remain unidentified – are minors living with their mother in another state, and that the archdiocese would assist the children with college costs.
Zavala emerged as a leading Catholic voice within the archdiocese and well beyond the southern California region on a wide range of social justice and human rights issues. He championed the needs of marginalized individuals, especially the poor, immigrants, incarcerated juvenile and adult offenders and condemned inmates. Through his leadership positions, he helped link the principles of Catholic social teaching to the work of promoting peace, conflict resolution and restorative justice. He was honored in 2004 by Death Penalty Focus for his statewide efforts to bring restorative justice reforms to the criminal justice system and to abolish the death penalty. In May 2011 he was recognized as a 'giant of justice' by Clergy & Laity United for Economic Justice (CLUE) for his social justice leadership at local and national levels.