Honda Red Bull Racing's Andrew Short won the $1,500 Progressive Holeshot Award, but Torco Fuels Honda rider Windham quickly passed him to take the lead.
San Manuel Yamaha star Reed came into the race 13 points ahead of Windham, but still recovering from his Detroit injuries sustained three races ago. The Australian's hopes of protecting as many points as possible then took a further hit when he crashed in turn one and remounted in last place.
But Windham also hit trouble soon after, with a trackside banner becoming tangled in his rear wheel while leading on lap two. The American was forced to stop and remove the banner, dropping him back to sixth place, but charged through the field and re-captured the lead on lap 17.
However, Reed snatched second place with a last lap pass on Short, giving him vital breathing room for the season finale.
"In the first turn, I crashed into the back wheel of Davi Millsaps' bike and fell down," said Reed. "When I was coming through the pack, I saw a bunch of Honda bikes and knew I was outnumbered, but I made the pass.
"It was absolutely wild out there tonight, the track was the rockiest I have seen in a long time and the racing was just vicious with people taking each other out everywhere. The hardest part about coming through the pack was avoiding other people's collisions.
"I am still not riding at my best as the shoulder is still very sore but I am looking forward to Las Vegas. I should have finished the job by now but I am pumped that the championship has come down to the wire – next weekend's event is going to be exciting," Reed concluded.
"I rode great tonight," said Windham. "I wish I came away with more points, but that's how it goes. I am excited to go to Las Vegas next week. It's going to be a great race."
Seattle also saw the season finale for the Western Regional AMA Supercross Lites championship. Suzuki's Ryan Dungey won the main event, but still couldn't prevent Jason Lawrence taking the title.
Team Solitaire's Bobby Kiniry won the Progressive Holeshot Award with Dungey in second while Lawrence, who came into the race with a six-point lead over Dungey, in fourth position.