Paul McGrillen opened the scoring for the home side after 30 minutes when he chipped the advancing Derek Jackson after Martin Lauchlan picked out his cross-field run.
The Shire thought that they had equalised two minutes later when Steven McGregor put the ball into his own net, however the assistant referee had flagged for offside before contact was made.
At half time the score was 1-0 and was a repeat of the last time when the sides met and Stenhousemuir romped home that day 6-0.
Within two minutes of the resumption the Shire were level and there was a touch of fortune to the goal as a Ross Donaldson cross looked to be drifting in but Willie McCulloch managed to tip the ball away but it hit Scott Livingstone and just crossed the line before being scrambled clear.
The assistant referee indicated that it was a goal immediately much to the chagrin of the Stenhousemuir players.
On the hour mark McGrillen scored his second with a similar goal to his first and the Shire suffered a double blow as keeper Jackson was injured in his attempt to stop the ball entering the net.
The Shire did not give up though and Donaldson scored with a cross-cum-shot that deceived McCulloch and landed in the net.
They then had a couple of good chances to win the game through Donaldson and Derek Ure before McGrillen headed home from close range for his and Stenhousemuir's third goal.