Dons boss Derek McInnes made three changes to his starting line up following the Dons' 0-0 draw with Rangers at Ibrox on Saturday afternoon. New signing Ronald Hernández was given his debut, Jon Gallagher and Ryan Hedges also coming into the XI. Shay Logan, Funso Ojo and Niall McGinn all moved to the subs' bench.
Following their rollercoaster 3-3 draw with Hearts in Perth on Saturday, eighth placed St Johnstone also made three changes to their team, with Callum Booth, Jason Holt and Michael O'Halloran replacing Liam Gordon, Scott Tanser and Chris Kane.
The Dons made a sharp start, begun by a run from Matty Kennedy. When that broke down, the Dons still kept Saints penned in, Hedges finding Gallagher who fired into the side netting in the second minute.
But it was the visitors who snatched the lead after six minutes, one ball on the counter-attack slicing Aberdeen open, Craig's pass from just inside his own half setting McCann away completely free through the middle and he advanced on goal to clip the ball past the exposed Joe Lewis.
The Dons looked shell shocked from there and Saints looked to take advantage, keeping Aberdeen pushed back, winning a free-kick just outside the box and then a corner but fortunately, the hosts survived. Gradually, they started to turn the tide and have more of the ball, but that early goal had left them with plenty to do.
Things got worse in the 19th minute when Ash Taylor went down, needing treatment on his left leg, but that proved fruitless and Michael Devlin was quickly introduced to the action in his place.
May and O'Halloran combined neatly down the right after a free-kick in the 21st minute, O'Halloran making a hash of his shot at goal, much to Aberdeen's relief. Saints were still looking sharp on the break, Wotherspoon firing straight at Lewis a minute later. It became one change each in the 27th minute when O'Halloran went down with a similar injury to Taylor and he limped off to make way for Wright.
The home side won a first corner in the 32nd minute after some good, patient build up play. Kennedy played the ball into the near post, Scott McKenna glancing a header just wide.
The Dons were almost on terms in the 42nd minute, Hernández's throw to Hedges allowing the Welshman to turn inside and find a clean first time strike with the left foot, Clark batting the ball to safety, by far Aberdeen's best moment of the half.
Aberdeen kept the pressure on, winning two corners in injury time. There were good deliveries from Hedges and then Kennedy, but Saints survived them both and got to the break still a goal to the good.
HALF-TIME: ABERDEEN 0 ST JOHNSTONE 1
Aberdeen made their second change ahead of the second half, Gallagher replaced by McGinn as the Dons went looking to get back on terms.
They almost did so in the 49th minute, Kennedy driving through the middle before feeding Sam Cosgrove. He was forced a shade too far wide but still got a shot away, Clark saving with his feet.
There was much more urgency about Aberdeen now and greater territorial control too as Saints dropped back in numbers to protect their lead. The visitors were defending well, all in their own half, space at a premium for the Aberdeen players. That sheer weight of numbers saved them in the 57th minute when McGinn played a fine cross through the box that took a fortunate deflection clear off McCart.
Ralston collected the game's first yellow card for dissent, screaming in the face of the assistant referee on the hour mark when he didn't get a corner decision go his way. Saints made their second change a minute later, May replaced by Kane, then McGeouch went into the book for a clumsy challenge on Holt.
The Dons made their final change of the night in the 66th minute, Hernández replaced by Bruce Anderson. That upped the tempo again, Aberdeen winning a fourth corner in the 70th minute, Saints clearing their lines again as Aberdeen struggled to end their goal drought.
Kennedy was hacked down by McCann in the 76th minute, the goalscorer going in the book as Aberdeen tried to find a way through. The free-kick almost brought the equaliser, McGinn's ball in worming its way through to McKenna in the six yard box, but he couldn't get a clean enough contact on it, giving Clark the chance to push the ball clear.
A 60 yard run from Ferguson got him into the box from where he won an 81st minute corner, McCart defending it well at the back post. From there, the Dons huffed and puffed but St Johnstone looked increasingly comfortable with each passing minute.
Aberdeen won a free-kick on the edge of the D in the 91st minute, McGinn's terrific effort curling over the wall, smacking against the inside of the post before bouncing away to safety.
In the end though, it was a carbon copy of last month's defeat to Motherwell, a poor goal conceded making for a long night against a massed 11 man defence which the Dons simply couldn't break down. It was all the more frustrating with Motherwell being thrashed 4-0 at home to Celtic, the Dons passing up the chance to go back into third place in the table.