Murray Davidson slotted home from close range on 58 minutes after the visitors failed to deal with a corner, before Gregory Tade sealed the points five minutes from time.
Just 2,425 fans watched the Perth side complete a hat-trick of victories over Kilmarnock this term and there was scant attacking threat from the Ayrshire side to threaten any other result.
Davidson's cut-back had given Rowan Vine the game's first chance, the striker skewing wide, before William Gros struck from range at the other end in what proved a rare first-half Killie foray.
Vine spurned his finest chance midway through the first half when he thrashed high into an empty stand from 12 yards and Cammy Bell's quick reactions soon after denied Steven MacLean to somehow preserve stalemate.
The interval failed to halt home momentum and after Sammy Clingan struck agonisingly wide of an upright, a set-piece brought the breakthrough when Liam Craig's corner found its way to Davidson at the back post.
A teasing Gros cross clipped Steven Anderson and almost brought unlikely parity but Bell's quick reactions when MacLean was through on goal made Saints wait for their second.
Craig was again the provider and Tade the unmarked man in the box who met his cross and settled any nerves.