Kawasaki's Kelly Smith took the $1,500 Progressive Direct Holeshot Award to begin the 20-lap main event in front, with injured championship leader Chad Reed taking the advantage later on in the lap.
The Australian held his position until lap four, when he lost momentum in the whoops section - allowing Windham to pass. Reed stayed close to the Honda rider until lap 9, after which Windham pulled steadily away, while Reed held on to comfortable second place ahead of Andrea Short.
"Tonight I just wanted to put myself into a good position," said Windham, who is now 13 points behind Reed with two rounds to go. "[Chad] put himself in a good position to not lose too many points tonight. It's all about me now and I feel good about the ride I put in tonight. I'm giving it all I can and that alone feels good."
"Man I glad that's over!" Reed admitted. "Tonight's race was a true test of the treatment I've been receiving all week and although we thought it was working I knew I wouldn't know for sure until I got out there for the race.
"I really pleased with the progress we have made in the seven days since the crash.
"My shoulder's definitely a lot better than last weekend. I just couldn't make it happen in the whoops. I didn't want to lay [the bike] down, so I rode for second tonight. I want this title and I'm not about to let it go. I feel like I've let these guys into this points' battle all season long by making mistakes.
"I looking forward to making amends on those mistakes over the next two races," Reed added.
Reed will resume treatment for his shoulder over then next few days before preparing for the penultimate round of the championship at Seattle's Qwest Field on Saturday 26th April.
Meanwhile, a clash between title rivals Trey Canard and Ryan Villopoto saw the former clinch his first-ever AMA Supercross Lites championship, with a win, in St Louis.
