Shire opened the scoring in the third minute from a Chris McGroarty corner. His centre was flicked on by Mark Tyrrell and Ross Donaldson's overhead kick left William McCulloch stranded.
The visitors' reply was a Kevin Struthers header from a Paul McGrillen cross - but the crossbar saved the day for Shire.
The home side doubled their advantage after 20 minutes from a free-kick that Donaldson took quickly to release McGroarty, who ran in on goal to score from eight yards.
The Warriors' Greig McCulloch had a shot deflected onto the crossbar but Shire retained their two-goal lead at the interval.
The visitors reduced the deficit with a cross-cum-shot by McGrillen which found the top corner with keeper Derek Jackson looking on.
But Paul Ross restored Shire's two-goal cushion with a deflected drive from the edge of the box after 68 minutes.
Shire could have put the issue beyond the opposition when Robbie Henderson was red-carded as the last defender for up-ending Derek Ure.
McGroarty's spot-kick was saved by substitute keeper James Kirkham, but Stenhousemuir failed to capitalise on their reprieve and their second goal, from Steven McGregor in injury time, was no more than a consolation.