Siller later died rescuing people from the Twin Towers.
Runners said the event is a legacy for Siller and all of the men and women who died that day.
"It's an honor, it's a real honor to be here. I mean we joined up for 9/11, I joined up afterwards. We were gonna go do something out in the other side of the world and it's great to come back here and still be a part of this after what happened," said one Iraq veteran.
"From the minute you go on the buses to when you're standing in line, people talk about were they're from. If someone needs their shoe tied in the tunnel, people stop, someone's walking, nobody pushes, it's always, 'excuse me' and great to see the kindness in people," said one race participant. This year's run comes a day after a truck carrying 18,000 shirts and materials for the race caught fire and destroyed or damaged all that was inside.
Siller's brother, Russ, says the incident won't stop the race.
"You start to prioritize and you realize what's a small problem and what's a big problem and so you know, shirts burning is not a big problem, rain is not a big problem -- 9/11 was a big problem," Siller said.
A total of about 20,000 runners came out for the race.
The annual event has raised more than $5 million since it began eight years ago.
The Brooklyn Battery Tunnel will be closed to traffic until 3 p.m. Sunday.