The Saints came excruciatingly close to their first victory of the AFLW season at Blacktown Oval on Wednesday night when Tarni White booted them ahead with three minutes remaining.
But a free kick and 50m penalty allowed the Giants to march downfield in the dying seconds before Smith cooly nailed the opportunity to secure a 6.5 (41) to 5.9 (39) result.
Several times GWS looked poised to pull clear, including when Cora Staunton drilled her third major to begin the final term, but the spirited Saints kept lifting in a tit-for-tat affair.
Considering both teams were coming off performances in which they failed to kick a goal and posted their lowest-ever scores, it was a much-improved effort all around.
"We dominated contest and clearance in the third quarter but their player behind the ball was hurting us a little bit, so we changed up a bit structurally - coach's error," McConnell said.
"I fuelled a little bit what was going on with their win around the ball, so that's probably on me.
"They got a head of steam and we looked like we weren't going to be able to stop it.
"Our ability to execute fluctuates a bit too much, but in the end we executed under extreme pressure."
McConnell and St Kilda coach Nick Dal Santo said they hadn't closely reviewed the 50m penalty call.
"I saw one of our players go down off the ball, but I can't tell you," McConnell said.
Dal Santo commented: "I saw two players go down and clearly it went one particular way".
The disappointed yet proud Saints mentor made no excuses for his young team.
"We had enough opportunities to keep the ball in our forward 50, let alone put another score on the board to give us a little bit of a buffer," he said.
"All losses are hard and that one hurts a little bit."
After heavy defeats to Adelaide and Melbourne, scoring only one goal across the games, a strong start was crucial for the Giants and Staunton provided it from a free kick at the top of the square.
She added another major in a scrappy first half - reaching eight goals for a third straight season - while GWS' Nicola Barr and Saints pair Nicola Xenos and Ashleigh Richards also kicked true.
Louise Stephenson slotted the Sherrin through the middle of the posts to open the third quarter for the Giants but Xenos again returned serve to set up a thrilling finish.
Just when Staunton had nearly put the match beyond doubt, Caitlin Greiser and White pushed the Saints to the verge of a long-awaited triumph.
But Smith's goal created history as the first to decide an AFLW clash after the siren.
