Leigh Griffiths netted the winning goal from the penalty spot in the 72nd minute after referee Willie Collum had penalised Jim Goodwin for a challenge on Matt Done, a decision which stunned Goodwin.
The home side, who were unbeaten in four games, started on the front foot but were kept at bay by some solid defending from Jorge Claros and Paul Hanlon for the visitors.
Griffiths had the first decent chance of the match for Hibs when he headed wide, while Graham Carey fired a free-kick straight at visiting keeper Ben Williams at the other end.
A decent period of pressure from Hibernian saw Griffiths clip the post, after surging past two defenders, and Claros send a shot wide.
But it was St Mirren who finished an even first half the stronger with Paul Dummett heading wide before Esmael Goncalves drew a smart save from Williams after a marauding run forward.
Griffiths threatened again for Hibs just past the hour after an uneventful start to the second half but his free-kick was safely gathered by Buddies goalkeeper Craig Samson.
Samson could then do nothing to keep out Griffiths' spot-kick although he did deny the striker with a smart save shortly afterwards.
St Mirren pushed hard for an equaliser in the closing stages but the visitors held firm for three welcome points as they moved up to fourth place.