Michael Duberry handled inside the Saints box from a corner and Simon Mensing converted the spot-kick with 22 minutes remaining.
Saints were presented with yet another golden chance with 12 minutes remaining as Mackay's corner fell to Michael Duberry 12 yards out.
Hamilton found the St Johnstone defence difficult to pass, with Michael Duberry and Steven Anderson limiting Accies' chances at breaching Peter Enckelman's goal.
St Johnstone manager Derek McInnes handed a debut to new signing Michael Duberry, with on-loan Bolton youngster Mark Connolly a place on the bench.
Dave MacKay and Sheridan missed the target for Saints early in the second period and Michael Duberry and Chris Millar drew saves from Stack.
After Michael Duberry had pulled one back for St Johnstone, referee Charlie Richmond awarded a free-kick against Steven Robb for a challenge on Kenny Deuchar.
St Mirren were 2-0 ahead thanks to strikes from Graham Carey and Andy Dorman before Michael Duberry headed in a scrambled goal for the Perth side on 79 minutes.
Michael Duberry and Steven Anderson kept Accies strikers Mickael Antoine-Curier and Damian Casalinuovo at bay but the visitors did manage a shot on target in the 30th minute.
Michael Duberry scrambled a shot off the line from the impressive Parlour and Wiltord had an effort ruled out for offside after Henry's shot had struck wood once more.
Hibs finally began to show some attacking intent as the half drew to a close, but their strikers couldn't find a way past the impressive-looking Michael Duberry and Graham Gartland in the Saints defence.
Cillian Sheridan joined on-loan from Celtic in January to bolster the attack, experienced former Chelsea defender Michael Duberry was another mid-season capture and both played starring roles in the memorable 5-1 win over Hibs in February.
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