Hutchison finished from 12 yards after he was bundled over by Saints winger Nathan Dyer two minutes from time.
Grzegorz Rasiak looked to have sealed all three points for Saints with his second goal for the club but it proved in vain.
In an uninspiring and frustrating game, it was the away side who took the early initiative.
On 16 minutes World Cup-bound Trinidad striker Stern John went past Jermaine Wright and Claus Lundekvam before delivering a low left-foot shot which Paul Smith did well to save.
Saints fashioned their opening effort just two minutes later when Andrew Surman drove the ball wide from the 18-yard line.
Rasiak then headed straight at Marton Fulop from substitute Darren Potter's corner moments later.
Both teams struggled to gain a grip on the match as the ball was passed ineffectively from defence to defence.
On 39 minutes, however, Richard Shaw thwarted Kenwyne Jones with a fantastic last-ditch challenge but referee Phil Dowd ruled otherwise and awarded a free-kick on the edge of the area.
Danny Higginbotham stepped up and hit a swerving, dipping effort which Fulop did well to save.
Saints boss George Burley introduced Dexter Blackstock at the expense of Jones and the young striker paved an opening for Surman to miss the best chance of the game on 56 minutes.
The South African born midfielder controlled Blackstock's cross and with just Fulop to beat hooked his volley wide.
Surman then atoned for his miss by delivering the decisive free-kick for Rasiak to head into the top corner to wake up the St Mary's crowd.
Two minutes from time Dele Adebola looked to have snatched an equaliser only for Lundekvam to block from five yards, but in the ensuing melee Dyer, showing his inexperience, dragged down Hutchison.
Dowd had no choice but to point to the spot and Hutchison equalised.