Cedric Anderson shot Karen Elaine Smith and eight year old Jonathan Martinez with a large-calibre revolver at North Park School before killing himself.
Most Rev Gerald Barnes wrote on Twitter: "I'm praying for the victims and entire school community after today's tragic shooting @NorthPark Elem. May God console us in this time of sorrow."
Mr Anderson and Ms Smith had been estranged for at least a month before the attack on Monday, in which a nine year old was also hurt.
The Diocese of San Bernardino later held a prayer service at Our Lady of the Assumption in the city, which touches the eastern tip of Los Angeles.
Maria Garcia, a spokeswoman for the San Bernardino City Unified School District, paid tribute to Ms Smith, saying: "It takes a very, very special person to be a special education teacher."
"We want her to be remembered for the amazing teacher that she was."
Mr Anderson, who had a criminal history that included weapons charges and domestic violence, walked into North Park telling staff he had something to drop off to his wife.