Issac Osbourne and Jonny Hayes provided the goals but the score does not come close to describing the visitors' superiority, particularly in a second half where Aberdeen controlled the play in the St Johnstone half and created numerous chances.
Nigel Hasselbaink added a late consolation for the hosts, but the defeat from the season home opener leaves St Johnstone with only a point from their first three SPL games.
Before kick-off St Johnstone boss Steve Lomas was dealt a blow as illness prevented Craig Beattie from making his debut.
Instead, Lomas went for Sean Higgins through the centre in a three-man attack that featured Hasselbaink and Liam Craig cutting in from either wing. Gregory Tade and Rowan Vine missed out through suspension.
An injury to Niall McGinn forced Aberdeen manager Craig Brown into a similar line-up reshuffle. Ryan Fraser came in and started on the left of a three-man attack with Scott Vernon through the middle and Jonny Hayes on the right.