Two goals from Stevie May and one from Nigel Hasselbaink earned the victory against a Killie side who had both Jackson Irvine and Darren Barr sent off.
Saints created the first decent chance of the game after 16 minutes when David Wotherspoon saw his long-range half-volley saved by Craig Samson.
Killie keeper Samson then kept out Hasselbaink's header but he could do nothing to deny the in-form striker in the 24th minute as the Dutchman latched on to Wotherspoon's incisive pass and calmly slotted home.
May then netted his 10th goal of the season in the 31st minute when he struck from 12 yards after taking advantage of some poor Killie defending, youngster Mark O'Hara failing to deal with Gary Miller's pass.
The visitors, who are still seeking their first away win of the season, had their first effort on goal in the 34th minute but Saints keeper Alan Mannus saved Kris Boyd's powerful effort.
The hosts took command again after the restart as May tested Samson and any hopes of a Kilmarnock comeback were ended in the 52nd minute when midfielder Jackson Irvine was sent off for a second bookable offence for slashing down Chris Millar.
Saints quickly made the most of their extra man by adding a third goal in the 54th minute, May netting from the penalty spot after Chris Millar was brought down by Jeroen Tesselaar.
Sean Clohessy pulled a goal back for Kilmarnock in the 69th minute when his cross from 25 yards drifted over Mannus and into the net.
The impressive May went in search of a hat-trick in the closing stages but his dipping volley went just wide and he was also twice denied by Samson, while Gwion Edwards saw a shot cleared off the line.
Kilmarnock's misery was complete in the 86th minute when Barr saw red, also for a second bookable offence, following a foul on May.