Former St Mirren midfielder Kyle Magennis was the shoot-out fall guy as Stephen Robinson's side edged past Kilmarnock into the Premier Sports Cup semi-finals.
Substitute Magennis saw his spot-kick saved by Shamal George before Malik Dijksteel despatched his effort to seal a 5-3 triumph after a 2-2 draw at Rugby Park.
The winning penalty sparked a pitch invasion from dozens of Buddies fans as they celebrated their first semi-final trip in 12 years.
St Mirren lost in the semi-finals of both cup competitions in the Covid-affected 2020-21 season but fans have not enjoyed a big day out at Hampden since their team won the League Cup in 2013.
The Paisley side led twice in the 90 minutes through impressive goals from Mikael Mandron and Jayden Richardson but Killie levelled late in each half, from a Robbie Deas header and Bruce Anderson's penalty.
The opening two minutes set the scene for an entertaining quarter-final as Jonah Ayunga knocked a cross into the side-netting before St Mirren goalkeeper Shamal George saved from David Watson at the other end.
The action kept coming. Mandron twice came close before former Saints midfielder Greg Kiltie curled inches wide.
The opener came in the 25th minute after Richardson cut out a cross and launched the ball forward for Mandron. The striker showed great skill to lob the ball over the head of Lewis Mayo before drilling into the far corner.
Killie levelled in the 44th minute when Dom Thompson sent in an outswinging free-kick and Deas got a run on Richard King before steering a header into the top corner.
Killie goalkeeper Max Stryjeck produced a brilliant reaction save after the interval to push a first-time effort from Killian Phillips on to the bar.
But the visitors - cheered on by 2,252 travelling fans - were back in front in the 59th minute as they kept the pressure on following a long throw. Richardson chested down a headed clearance before volleying into the top corner from 22 yards.
Stuart Kettlewell immediately brought on Anderson but the game was almost out of Kilmarnock's reach when they lost the ball immediately after the restart. Stryjek tipped over Ayunga's strike after Saints broke.
Anderson almost had a swift impact but Miguel Freckleton slid in to block the striker's goalbound effort.
After being stung by a stoppage-time VAR handball decision against Celtic last weekend, Killie thought they should have had a penalty when Thompson's free-kick appeared to strike the arm of Keanu Baccus.
The Australian's arm seemed to be right by his side and, with no video technology in use, referee David Dickinson gave a corner.
Declan John hit a free-kick just over for St Mirren, who saw skipper Mark O'Hara walk off injured. Liam Donnelly came on for his debut amid boos from the fans he had played in front of for the previous three seasons.
Mandron shot straight at Stryjek from 18 yards and Saints were made to pay when King brought down Marley Watkins as the substitute appeared from his blind side as the defender attempted to play the ball. Anderson blasted the 86th-minute spot-kick down the middle of the net.
There was plenty of aerial pressure at both ends in extra-time but, with seven draws between the teams in the opening five fixtures of the league season, it was no surprise the tie went all the way.