Mark McGuigan’s 80th minute goal was enough to secure three points against the Hedgemen who were already confirmed as club 42 prior to kick off and will meet either Kelty Hearts or Brora Rangers in a two legged play-off for their spot in the league later this month.
For Stenny though, they finish top of the bottom half of League 2 sixth in the overall table, just one point ahead of Albion Rovers who the lost to last Thursday at Ochilview.
In a game that was oveshadowed by the resulting controversy, Matthew Aitken netted the only goal of the on the 31st minute which was enough to bag the three points for the visitors.
New Stenny manager Stephen Swift was in the dugout for both games and will now begin the process of building a squad for next season that will be capable of a higher league finish and potential push for promotion.
With the bulk of the first team squad either out of contract or ending loan spells, the former BSC Glasgow boss will have the chance to build a new group from the ground up should he choose.
Meanwhile, the League 2 promotion places were confirmed on Tuesday night as Edinburgh City, Elgin City and Stirling Albion will join either Clyde or Dumbarton in the play-offs for a place in League 1 next season.
Queen’s Park were already confirmed as champions while Forfar Athletic’s relegation to League 2 was also confirmed for next season.