The incident occurred shortly before 10 a.m. (11 a.m. ET) as members of a small Kansas church that protests at military funerals and counter-protesters stood nearly a block away from First United Methodist Church during services for Staff Sgt. Michael Bock, 26, who died August 13 in Afghanistan's Helmand province.
A man in a Ford-150 pickup truck drove by, extended his arm and sprayed with a large can, police said. His vehicle was stopped a few minutes later.
"Initial indications are he was probably targeting the Westboro Baptist Church" protesters, said officer Michael Pecha, a spokesman for Omaha police.
Hear from a CNN iReporter hit with pepper spray at the event
George Vogel, 62, who lives just north of Omaha, was booked for 16 counts of misdemeanor assault and one count of felony assault on a police officer for the pepper-spray exposure, police said. Vogel also faces one count of child neglect because his child was in the truck, Pecha told CNN.
Westboro members, led by pastor Fred Phelps, believe God is punishing the United States for "the sin of homosexuality" through events including soldiers' deaths. Members have traveled the country, shouting at grieving family members at funerals and displaying such signs as "Thank God for Dead Soldiers," "God Blew Up the Troops" and "AIDS Cures Fags."
A 2005 protest by church members at the funeral of a Missouri soldier prompted state lawmakers to pass legislation criminalizing picketing "in front or about" a funeral location or procession. A federal judge earlier this month rejected Missouri's tight restrictions, saying they violated the free speech clause of the First Amendment.
It was unclear Saturday evening exactly who had been pepper sprayed, but a Westboro member said no one in her group was affected.
The incident occurred during the funeral and while nearly 600 members of the Patriot Guard Riders ringed the church and stood vigil, the group's state leader said.
Scott Knudsen, Patriot Guard Riders captain for Nebraska, said no members of the Patriot Guard had any interaction with the church members or counter-protesters, which he numbered Saturday at about 12.
"We don't get close to them," Knudsen said of the Westboro members. "We have our backs to them."
Patriot Guard members, who come when they are invited by families, shield families from distraction, Knudsen said.
"We don't condone counter-protesters," said Knudsen, adding he was troubled by Saturday's incident.
"It's inappropriate," he said. "It's a funeral service."
Pecha also said that there were no altercations between Westboro members and the Patriot Guard.
Shirley Phelps-Roper, a member of Westboro Baptist Church, said Omaha police did not adequately control roughly 30 counter-protesters, who she said jostled with church members. She also challenged Knudsen's and Pecha's account, saying a few Patriot Guard members were among the counter-protesters.
The group was about 1,000 feet from the church when the driver came by. "Of course it was directed at us," Phelps-Roper, who is Fred Phelps' daughter, said of the pepper spray.
None of the 16 Westboro members on the corner were affected because they raised signs to shield themselves or turned away, Phelps-Roper said. The group returned home shortly afterward.
Extra officers were on hand for any possible altercations, but there were only verbal exchanges before the truck drove up, police said.
CNN's Phil Gast contributed to this report.