With Saints trailing to Peter Pawlett's 17th-minute strike from long distance, Saints boss Tommy Wright threw on Fallon in the 70th minute but he was shown a straight red card by Willie Collum for an elbow on Michael Hector just over 60 seconds later.
St Johnstone had struggled to break down a resilient Aberdeen defence other than in one first-half moment when Jamie Langfield saved brilliantly from Stevie May, and the numerical disadvantage proved too much as Niall McGinn doubled the lead with a superb curler with five minutes left.
Aberdeen manager Derek McInnes, who was making his first competitive return to his former club, said of the flashpoint: "I have just seen it again there, just once, and I think there is a raised elbow there. Only Rory Fallon can tell if it was deliberate or not and in the referee's eyes it was."
McInnes, who lost Ryan Jack to a calf injury late on, felt his side were deserved winners despite the helping hand from Fallon, who left Pittodrie in the summer.
McInnes said: "We knew we would get chances to produce some quality and bring composure to the game in the last third and the two bits of quality for the goals were outstanding, two terrific goals.
"But that alone didn't win the game. It was all the fundamentals - the headers, the second balls, winning individual battles.
"All in all I think we were worthy winners. The sending-off took the wind out of St Johnstone a wee bit and helped us get over the line."