The affidavit said Capener apologized for stabbing the others after he was read his rights and agreed to speak to police.
Masons are a fraternal group involved in charity and other community activities, but many of their rituals and symbols are secret.
Capener was charged on three counts of aggravated battery and ordered held on $250,000 bail.
St. Jude Thaddeus' pastor, the Rev. John Daniel, said Capener's mother was "very active" in the parish and serves as a Eucharistic minister there.
"He was here occasionally but not very often," Daniel said.
Daniel said that Capener had just graduated from a community college and appeared to be doing well after getting a job. "I think he's been struggling for a while, maybe with some (mental) health issues," Daniel said.
Both Alvarez and Madrid remained hospitalized Monday and their families said the men were recovering from wounds that were described as not life-threatening.
Services at the 3,000-member church resumed Monday. Parishioners stopped to leave flowers, notes and candles outside the church and at the church's shrine dedicated to St. Jude, the church's namesake and the Catholic Patron Saint of "lost causes."
In Mass homilies throughout the day, Daniel said he compared St. Catherine of Siena, who worked for peace in 14th century Italy, with the power of forgiveness.
Robynn Madrid, whose husband Gerald Madrid was recovering from the attack, said despite the pain Capener caused, she's already forgiven him. "We're praying for his family," she said.
Spanish choir member Richard Aragon said he, too, is trying to show compassion and forgiveness, even though he had trouble sleeping the night after the stabbing. Aragon was preparing for the upcoming Spanish services when the attack began.
"There's nothing you can do. There's obviously something...he's touched or something," Aragon said. "It already happened. It's too late."
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