The death of Seau, a longtime player for the San Diego Chargers, was a blow to residents of that city where the retired linebacker was viewed as a successful native son who gave generously to his community.
Seau shot himself in the chest with a revolver on Wednesday in the bedroom of his house in Oceanside, just north of San Diego, police said.
About 400 fans, friends and family members of Seau paddled out into the Pacific Ocean in front of his house for the ceremony on Sunday. Thousands of spectators lined the narrow beachfront road known as The Strand, many of them wearing Chargers jerseys and carrying flowers.
For most of his 20-year career, Seau played for the Chargers before moving on to the Miami Dolphins and New England Patriots and retiring after the 2009 season. He was selected 12 times to play in the Pro Bowl (all-star game).
Among the surfers in the water on Sunday was New Orleans Saints quarterback Drew Brees, who earlier i n h is career played for the Chargers with Seau.
After the ceremony was under way and the surfers and three Hawaiian outrigger canoes formed a circle past the breaking waves, Seau family friend Jay Michael expressed concern that Seau was not represented in the paddle-out ceremony, which often includes the departed surfer's board.
Michael found someone with a key to Seau's garage, where seven surfboards remained neatly racked on the back wall, and he grabbed one of Seau's boards and rushed into the water.
"This isn't right," Michael said. "We got to do this up right - I'm bringing Junior's board."
Michael stood atop the bright yellow board with gray strips, and paddled it out to cheers from surfers in the water and people on the beach.
Seau often surfed the same waters where the ceremony was held, which is just south of the Oceanside Pier.
Memorial paddle-out ceremonies are a longstanding tradition among surfers in Southern California, Hawaii and other places.
Seau's death follows two recent high profile suicides of former National Football League players.
Former Chicago Bears defensive back Dave Duerson shot himself in the chest in February 2011 and asked that his brain be examined for evidence of injury from his playing days. Last month, retired Atlanta Falcons safety Ray Easterling, who was among hundreds of former NFL players suing the league over head injuries, killed himself.
The deaths have come at a time of heightened scrutiny of the league and the long-term effects on players of repeated blows to the head. Pastor Shawn Mitchell, a spokesman for the Seau family, had said last week they planned to have Seau's brain examined for evidence of injury, but this weekend he said the family was giving that decision further thought.
During his life, Seau ran a foundation named after himself that helped young people avoid drugs and alcohol, child abuse and delinquency and get an education. The foundation distributed nearly $4 million to organisations providing services for youths, according to its website.