Harrison Midda put Woodford ahead after five minutes after a cracking counter attack from James Ryan down the right.
David Grossman hauled FC Team back on level terms but Woodford dominated the second half and Ryan capped off a brilliant season with a wonder strike from 30 yards that crashed in off the bar.
Woodford chairman Alex Aviram told JC Sport: "We dedicate winning the Championship to the loving memory of the late Paul Hyams, aka 5 foot, who lost his battle to cancer in November 2015". He told JC Sport: "Our legendary ex-gaffer was a true Woodford hero and his voice will forever be heard in the our changing room and on our sidelines."
Joint-manager Daryl Kay told JC Sport: "Well what can I say other than a massive congratulations to the boys. I've said all year that were the best team in the league and today I was proved right, fact!
"FC Team showed up thinking they had the win in the bag today but we bossed them from start to finish. They're a good side, but not good enough, and we are, that was the difference.
"To lose only one game all season in game two, go another 17 games without losing is brilliant and the boys deserve all the plaudits.
"This has been a wonderful season for Woodford - my decision to keep the managers in-house with the appointment of Daryl Kay and Jerome Marks proved to be the winning formula. I'm very proud of what this club has achieved and only losing one game all season shows how hard work can pay off. Everyone in involved with this season are true warriors."
FC Team player-manager Mitch Young told JC Sport: "Congratulations to Woodford - they have been the most consistent team all season and have thoroughly deserved to win the league.
"We somehow found ourselves in a shot of winning the league after a poor first half of the season but we let the occasion get the better of us today.
"We were not composed and failed to create meaningful chances. Saying that when we did create a few chances we missed them and in games like this it is crucial.
"We will work hard to finish runners-up and there will be no shame in that, but my players will look back at this season and feel with the players we have, we should have done it."
