Tommy Taylor's injury-hit troops more than held their own against The Stutes, but second half substitutions saw Lynn lose their way in the final quarter of the match.
Taylor emerged from the dressing room happy with his side's final pre-season showing, saying: "We had four or five players out, but Histon weren't any better than us over the 90 minutes.
"I thought we defended well and dealt with more or less everything they had to throw at us. If we'd had a few more people wanting to pick the ball up in the second half then I think we would have won."
With Grant Cooper, Paul Kelly, Dean West, Jack Defty and Robbie Harris all missing from the starting XI, many Lynn fans expected the worst against last season's league champions.
But The Walks outfit silenced the doubters with an assured display in the first hour of the match, with Simon Clark and Cedric Anselin both impressive.
Midfielder Sam McMahon also made a 65-minute return to give Lynn some extra bite in the middle of the park.
Midway through the first period, John Higgs superbly tipped former Linnet Ian Cambridge's header onto his post before a combination of the goalkeeper and Mark Camm somehow managed to scramble the ball clear.
Anselin forced Lance Key into action in the 31st minute before setting up Danny Bloomfield, only for the striker's first touch to let him down three minutes later. Higgs pulled off another fine stop to deny another ex-Walks player in Colin Vowden, who also saw his volley whistle just past the post early in the second period.
Lynn went on to enjoy their best spell of the game, with Stewart Roach failing to convert a Mark Angel centre and Clark sending a powerful header an inch over the Histon crossbar.
The Linnets eventually took the lead when Anselin and Angel combined to feed Roach, who punished some hesitancy between Roscoe Hipperson and Key with a smart finish.
Lynn replaced McMahon with Adam Kirby, who has now signed for Newmarket in the Ridgeons Premier League, and Anselin with Stephen Harvey and the game swung back in Histon's favour.
The home side's Matthew Haniver had an effort ruled out for offside and shortly after Vowden thundered a header against the bar.
With eight minutes remaining Cambridge pounced at the back post and six minutes later another set piece led to home substitute Leon Gutzmore netting the winner.
Histon: Key, Jackman, Goddard (McAfferty 86), Hipperson, Vowden, Nightingale, Haniver (Knight-Percival 81), Andrews, Kennedy (Gutzmore 81), Barker. Subs not used: Coe, Summerscales. Goals: Cambridge 83, Gutzmore 85.
Lynn: Higgs (Benstead 45), Jones, Smith, Camm, Clark, C. Defty, McMahon (Kirby 65), Anselin (Harvey 76), Roach, Bloomfield, Angel. Subs not used: Hyde, McNeil. Goal: Roach 65.
Referee: Graham Horwood (Luton). MoM: Simon Clark.
Bookings - Histon: Nightingale; Lynn: Clark and McMahon.