The Colts went into Saturday knowing a point against Brigg Town CIC would be enough to secure the title.
However, opponents Brigg were unable to raise a side, meaning Wyberton were awarded three points.
It was a frustrating end for the Colts, who also saw opponents Nunsthorpe Tavern and Immingham Town not travelling in recent weeks.
But joint-manager Jon Macleod didn't let it take the gloss of the achievement.
"Amazing! What a bunch of players, from start to finish," he said.
"The three games where they didn't travel, there's nothing we can do about that."
Wyberton, who won the Lincs Junior Cup eight days earlier missed out on a treble when they were beaten 3-1 by Lincoln Moorlands Railway in the Supplementary Cup on Wednesday at Skegness Town's Vertigo Stadium.
Liam Bentley, Joe Aitken and Elliott Shearwood were the Railway's matchwinners with Liam Ogden netting for the Colts.
However, Macleod is now hungry for more glory.
He added: "Hopefully everyone will stay. We need to bolster the squad, we know that. But we're here to win."
Joint-boss Jamie Hanton added: "You win one thing you want more.
"We want to defend it. It's never easy."