A match of few chances at Pittodrie was settled with an early goal from Ryan Jack, although Saints were unfortunate not to earn a share of the spoils.
The Dons struck after just eight minutes when midfielder Jack unleashed a low drive from 25 yards past Alan Mannus.
Adam Rooney then tested Mannus with a shot from outside the penalty area and two minutes later Jamie Langfield was tested by David Wotherspoon, but the Aberdeen keeper easily saved.
Saints came close to an equaliser nine minutes before the break when Stevie May kept the ball in play and set up Michael O'Halloran, but he shot narrowly wide.
O'Halloran came even closer to a goal on 66 minutes when he burst away from Alan Tate and smacked a shot off the inside of the post.
St Johnstone's frustrating afternoon was completed when substitute Steven MacLean was sent off for two mistimed challenges on Barry Robson and Nicky Low.