Charles Richard Jennings Jr., 35, was captured Sunday afternoon in nearby Box Elder County after fleeing in a stolen pickup truck, investigators said.
Witnesses say they heard one gunshot during the 11:30 a.m. Mass on Sunday at Saint James the Just Catholic Church in Ogden, and that parishioners immediately hit the floor.
The victim was taken to a hospital, where he was listed in critical but stable condition. His name wasn't immediately released.
Police said the victim was deliberately targeted by the gunman and it wasn't a random act of violence.
"We don't know the motive," Ogden police Lt. Danielle Croyle told The Salt Lake Tribune. "It is a domestic violence-related incident."
Parishioner Rebecca Ory Hernandez said the congregation was told by a priest that the suspect and his wife had been involved in domestic disputes.
Hernandez was sitting close to the victim when the shooting occurred, she said.
"The guy walked up to his father-in-law and shot him point blank in the head," Hernandez told Ogden's Standard-Examiner. "Then I ran over to the victim and pulled my scarf off and put it around his head.
"He was pretty calm. There was so much blood ... People were in shock and some people were passing out. We have some military guys in our parish and they ran out after the guy," she added.
Parishioner Leon Bedford said the victim was sitting in a back pew with his wife when their daughter and son-in-law walked in holding hands as the congregation started saying a prayer.
"Oh, it's obvious it was well planned out," Bedford told the Standard-Examiner. "They came into the church hand in hand, and he walked right up to (the victim) and pulled that trigger. We just hope and pray that he makes it."
Jennings is accused of stealing the truck at gunpoint from a nearby resident after fleeing the church. He was booked on charges of attempted aggravated criminal homicide and aggravated robbery.
Further details about the shooting will not be released until a news conference Monday morning at McKay-Dee Hospital, officials said.
A family spokesperson and a police representative will be on hand to discuss the case and status of the victim, hospital spokesman Chris Dallin said.