St Johnstone recorded five straight league wins for the first time since 1971 with Kilmarnock the latest victims of the Perth side's impressive form.
Murray Davidson scrambled home Saints' opener after Cammy Bell had saved Steven Anderson's header.
The visitors almost levelled when Cillian Sheridan struck the post.
Nigel Hasselbaink netted the home side's second in the 90th minute before James Fowler pulled one back for Killie in injury time.
Steve Lomas's side move up to second in the Scottish Premier League, three points behind Celtic, while Kenny Shiels' Kilmarnock are seventh.
Anderson should perhaps have done better than head wide from Liam Craig's free-kick as the home side sought an early breakthrough.
Craig had a shot blocked by team-mate Gregory Tade before taking the corner that led to the opener.
The delivery was nodded powerfully towards goal by Anderson and, though Bell made the block, the goalkeeper could not prevent Davidson forcing the ball over the line.
Killie came back into the match and Sheridan's free-kick cracked off Saints keeper Alan Mannus's right-hand post shortly before half-time.
Bell denied Davidson a second with a diving save eight mintues after the break and the keeper then blocked an effort from Hasselbaink.
Rowan Vine curled over the Kilmarnock bar and Hasselbaink was then guilty of a glaring miss as Saints sought to make sure of the points.
Tade beat the offside trap and drew Bell before squaring for Hasselbaink but the Dutchman allowed the ball to ricochet off his shin and slip wide of the open goal.
Hasselbaink's frustration continued when his next shot was saved but, after Sheridan's drive stung the palms of Mannus, the Saints forward eventually added his name to scoresheet.
Tade was again the provider with the through pass and Hasselbaink managed to get his strike beyond Bell.
Fowler's deflected effort temporarily gave Kilmarnock hope but St Johnstone saw out the remainder of injury time to emulate the run of five successive league wins last recorded under Willie Ormond's management.