Clyde defender Neil McGowan brought then felled Robert Love in the box to earn the visitors a penalty.
Kevin Motion converted the spot-kick then Stenny made their win safe when Jordan Smith smashed home after 64 minutes when Clyde failed to clear.
Clyde: Findlay , Park (Wilson 14), Neil McGowan, Kinniburgh, Lithgow, Stevenson (White 67), Strachan, McLachlan, John Stewart (Sawyers 67), Doolan, Higgins. Subs Not Used: Allan, Cassidy.
Stenhousemuir: McCluskey, Lyle, Stephen Thomson, Gibb, Smith, Thom, Love (Quinn 86), Iain Thomson, Dalziel, Pat Scullion (Dickson 79), Motion. Subs Not Used: Bennett, Stirling, Plenderleith.
Booked: Stephen Thomson, Love.
Goals: Motion 20 pen, Smith 64.
Ref: C Charleston