Brian Carrigan and Brian McPhee set up Pat Keogh for a low cross-cum-shot which was sliced into his own net by David van Zanten.
The Accies had always looked the likelier side, attacking with speed and precision. McPhee had a header cleared with the assistance of a post and Craig Hinchcliffe before Andy Millen hacked the ball away for a corner.
Saints replied with a van Zanten cross which Mixu Paatelainen headed back for Simon Lappin but the wing-back failed to find any purchase on his volley.
Mark Corcoran was outstanding throughout and a surging run from the tricky forward provided a cross from Mark McLaughlin which was plucked out of the air by Hinchcliffe before McPhee and Scott Tunbridge could capitalise.
Mark Reilly came to Saints' rescue when he headed out a fierce Corcoran drive after the Accies' dangerman had burst between van Zanten and Ricky Gillies in a thrilling run.
Saints came more into the game after the break but they did not test David McEwan in the Hamilton goal.
The introduction of Carrigan injected more potency into Accies' attacks and the goal was partly due to his intervention.
Desperate Saints won free-kick after free-kick, but McEwan rose to the occasion with two outstanding saves to deny Millen and Stewart Kean.
The frustration felt by the home side was illustrated when manager Gus MacPherson attempted to ensure a quick throw-in was taken, but was obstructed by Hamilton staff, causing a scuffle which had police stepping in.