The Buddhists endured subfreezing temperatures to hold the rite at Jogye Temple, the headquarters of the Jogye Order, South Korea's largest Buddhist sect.
Some monks clad in gray and saffron robes offered white chrysanthemums -- a traditional Korean symbol of grief -- and bowed in front of photos of animals inside the temple in central Seoul.
They also bowed toward two big golden statues of Buddha and chanted sutras before circling around a pagoda and burning mortuary tablets and incense.
The animals -- mostly pigs -- have been killed in an attempt to halt the outbreak, which was reported in November, according to the Ministry of Public Administration and Security.
The highly infectious disease is often fatal for cloven-hoofed animals including cows, sheep, pigs and goats, causing blisters on the mouth and feet.
A monk named Hyechong said the temple held the rite to help guide the spirits of the animals to heaven.
"We have to do our best to make animals infected with foot-and-mouth disease die peacefully with the help of the government and citizen's groups," he said, alluding to criticism that animals have been inhumanely killed.
Quarantine workers have administered muscle relaxants before killing the animals and burying them, said Park Yong-wook, a ministry official handling the issue. He said authorities vaccinated more than 4.6 million cows and pigs as part of efforts to halt the outbreak.
However, animal rights activists claimed that most of the pigs were buried alive. "We should not kill animals in this way," said Lee Won-bok, head of the Korea Association for Animal Protection.
A group of about 10 activists dressed in white and wearing animal masks in central Seoul called on the government to introduce more humane ways to kill the animals, said Gail Jun, an official of the Korean Animal Welfare Association.
After praying at the temple, Park Young-hae, 74, wrote a message of condolence on a small, white banner and attached it to a bulletin board. "I hope that the dead animals will go to paradise," she said.
Another banner read: "It must have been painful and you cried a lot. I hope that you go to a good place and enjoy happiness."
The disease last hit South Korea in January 2010 -- for the first time in eight years -- when more than 55,800 pigs and cows were killed, the ministry said.