The young Dons lined up with Tom Ritchie in goal behind a back four of Calvin Ramsay, Andy Paterson, Luke Turner and Lyall Booth. Max Barry and skipper were in the heart of the midfield engine room, flanked by Kevin Hanratty and Lewis Duncan, with Michael Dangana and Michael Ruth up top.
Aberdeen had the ball in the net after only 45 seconds but Hanratty was flagged offside. A great ball from Ramsay sent Hanratty scampering down the left and the Saints defence did well to snuff out the cross. From the resulting corner, Turner had the ball in the net, but again the goal was ruled out for an infringement.
Steele was booked for a foul on Dangana in the 6th minute, Barron's free kick well blocked by the wall. Hanratty was right in the mood and looked dangerous every time he got on the ball in the opening exchanges.
Hanratty's fizzing cross was flicked out of the reach of Dangana as the Dons pressed for the opener, Barron's corner picking out Turner, but his header lacked the power to trouble Wills.
Aberdeen were laying some lovely, flowing football but the final ball was just not quite falling to a man in a red shirt with Saints defending desperately. The visitors were forced to make a change after 19 minutes, Bisset coming on for left back Smith who had picked up a knock.
A slip from the Dons in midfield gave Walsh a chance to race forward for Saints, but Ritchie saved well. Shortly after Finnan had a pop at goal, his curling effort drifting off target.
On 28 minutes a wonderful run from Ruth saw the forward beat a number of defenders before firing in a powerful shot which was inches past the keeper's right-hand post.
The opening half-hour had been hugely entertaining, the game quite evenly balanced after the visitors had survived Aberdeen's powerful start. The main surprise was the lack of any goals.
Ruth fired over after a Barron corner then Hanratty hit a free-kick too high as the interval approached. A place in the semi-finals was very much still in the melting pot.
Half time - Aberdeen 0 St Johnstone 0
Saints coach Alan Maybury replaced Northcott with Moreland for the second half. Max Barry danced his way into the box, and it took a desperate block to prevent a goal. Aberdeen looked certain to take the lead but Saints then raced up the park and the ball was squared for John Moreland to fire low into the bottom corner.
A real sucker punch.
Aberdeen responded positively, Hanratty's dangerous ball inches from the reach of a posse of inrushing attackers. Ferguson lifted a shot over as the Pert side looked for a second goal which would give them breathing space.
Another dazzling run from Hanratty was thwarted by a blanket defence from Saints before a Barron free-kick just evaded Turner. At the other end a dangerous free-kick from the right was deflected just wide then Steele headed past from the ensuing corner when it looked easier to score.
Ruth missed a great opportunity as he headed Barron's corner wide on 63 minutes. Tyler Mykyta then replaced Duncan in the home ranks.
Play was becoming a little ragged as the match went into its final quarter of an hour and Hanratty was booked for a tug on the shirt of an opponent.
Dangana raced clear on the left but again his cross was snuffed out by the doughty Perth defence. They were helpless however on 77 minutes when Hanratty rifled Lyall Booth's cross high past Wills for the goal which Kevin and the team deserved. Left back Booth did really well to create the chance by beating his man and then put over an inviting ball which was met perfectly.
Game on for the final ten plus minutes.
It was nearly 2-1 on 82 minutes, Mykyta heading just over after another fine cross from Booth. The sub was injured in the process and had to go off to be replaced by Shanks.
Deep into stoppage time Wills made a great save from the outstanding Hanratty but the scores stayed at one apiece so extra time would be necessary.
Full Time - Aberdeen 1 St Johnstone 1
Barry Robson's side started extra time strongly.
Calvin Ramsay produced a good run to get to the by-line. The right back - who along with Hanratty and Ritchie have been named in the Scotland U17 squad today - showed good composure to look up and pick out the run of Dangana but his shot at the near post was blocked. Then from a Hanratty corner the ball bounced around the six yard box but again no one could force it home.
In the ninth minute of extra-time Michael Dangana produced a moment of real quality to turn the tie in the Dons favour. The striker with his back to goal picked the ball up, he turned and curled a superb shot into the top corner.
St Johnstone came back into it at the end of the first half of extra time and Tom Ritchie produced a brilliant save to tip a shot from Ferguson wide. It proved to be a vital stop.
Half time extra time - Aberdeen 2 St Johnstone 1
Aberdeen did well to control most of the game in the second period of extra time with Shanks, Dangana and Ruth working hard to hold the ball up in the other half.
As the game become really stretched it was Aberdeen who were able to make the game safe when Dangana showed good strength and skill to force his way into the area and when he was brought down referee Duncan Nicolson correctly pointed to the spot. Connor Barron stepped forward and coolly slotted the ball into the corner and despite Willis guessing the right way, he could not get near the inch perfect penalty from the skipper. It was Connor's 11th goal of the campaign.
St Johnstone, who were really well organised throughout, to their credit battled to the very end and both sets of players, who had given everything, looked shattered when the final whistle sounded.
For the second round in a row Barry Robson's side had shown real character and fighting spirit to keep their cup hopes alive.