After last Sunday's 3-0 win at Hearts, Killie triumphed in convincing fashion again as Michael Duberry deflected Ben Gordon's 36th-minute cross into his own net before Conor Sammon struck seven minutes from time and Liam Kelly added a third in stoppage time.
Cleveland Taylor, a first-half replacement for Murray Davidson, headed on to the top of the bar and hit another effort against the woodwork as Saints struggled in the final third of the pitch and suffered a third straight loss.
Davidson was one of five changes as Saints aimed to bounce back from successive 3-0 losses to Celtic, but soon the midfielder was limping off the field with an apparent recurrence of his ankle problem.
That was not the only worry for St Johnstone manager Derek McInnes.
A pitch inspection an hour before kick-off was passed despite the ball being unable to bounce on sections of the saturated surface, but it was no excuse for Saints' sloppy defending in the opening 45 minutes as Kilmarnock began brightly.
A mistake by Alan Maybury granted Kelly enough space for a shot, but Saints goalkeeper Graeme Smith saved at his near post.
Sam Parkin then missed a defensive header from Alexei Eremenko's cross and the ball deflected off Mohamadou Sissoko's shin and into the arms of Smith.
Smith saved from Craig Bryson and Sammon shot wide, while Andy Jackson spurned two half-chances for Saints.
Davidson was then penalised for a foul on Eremenko, the challenge earning him a booking and forcing him off to be replaced by Taylor after 26 minutes.
Taylor's looping header from Liam Craig's cross hit the top of the bar before going out for a goal kick, with Bell covering the danger.
The opener came after 36 minutes through the Chelsea connection - but not Jody Morris and Duberry, as St Johnstone fans would hope.
Killie left-back Gordon, on loan from Stamford Bridge, raced down the left unchallenged and the ball was deflected into the hosts' net off the outstretched leg of Saints centre back Duberry.
Smith then saved a Kevin Rutkiewicz header from a similar fate as Saints trailed at the interval.
With the hosts lacking the incisive edge, Killie continued to look the more dangerous.
Bryson saw an effort from 20 yards saved by Smith after the midfielder had fought off the challenge of Duberry.
But Taylor then hit the bar for the second time. From Duberry's knock down, he screwed a right-foot effort which was always rising against the woodwork.
Parkin appeared to be impeded from the resulting corner while making an aerial challenge but still Saints were denied.
Morris was booked after Eremenko lured a foul and the Finland forward found himself cautioned for continuing to debate the decision long after the initial incident.
Sammon had a 73rd-minute effort ruled out for a foul on Maybury on the edge of the area, but his goal came 20 minutes later.
Bryson fed Sammon and he twisted and turned beyond Duberry and Craig before tucking in between Smith's legs.
Sammon was booked for his over-exuberant celebrations, with Marcus Haber replacing Parkin.
Haber's participation soon ended though as an innocuous incident saw him require a stretcher to leave the field, resulting in five minutes of stoppage time.
And Kelly tucked in a third in the additional time after being set up by replacement Danny Invincibile.