The Killie captain headed the opener six minutes after the interval then was unlucky when his headed effort crashed off the post.
However, the big striker was not to be denied and he effectively sealed the points just after the hour mark with a volley from distance, catching Saints goalkeeper Alan Main out of position.
In the second minute of added time Killie defender Frazer Wright headed a Danny Grainger corner into his own goal but it was too late for the Saints who once again may argue that they did not get their just rewards.
The height and power of Kyle appeared to be Kilmarnock's most potent threat as the game gathered momentum, but in the 16th minute it was St Johnstone's diminutive midfielder Jody Morris who rose high to head Dave Mackay's cross over the bar.
Moments later Collin Samuel, playing the lone striker's role, shot from the edge of the box but his weak effort trundled through to home goalkeeper Mark Brown.
Grainger then burst into the Kilmarnock penalty area with some ease and Wright did well to prevent Samuel getting a clean shot in at the back post and the ball sliced wide for a goal kick.
On the half-hour mark Kilmarnock midfielder Craig Bryson went to ground inside the Saints box after a challenge by Chris Millar but referee Alan Muir ignored optimistic claims for a penalty.
Five minutes from the break St Johnstone midfielder Gavin Swankie drew a fine save from Brown with a curling shot from 25 yards but the half-time whistle came as something of a relief.
The second half began in scrappy fashion as Kyle clattered into Steven Anderson as the Saints defender cleared.
Moments later, in the 51st minute, as Anderson continued his recovery, Kyle put the home side ahead with the simplest of goals.
Garry Hay curled a long ball into the St Johnstone box and the Killie captain beat the hesitant Main to head into the empty net.
It was the first effective use of the route-one tactic but a more thoughtful approach nearly paid off three minutes later as St Johnstone wobbled.
Kyle latched onto a searching cross from Hay to crash a header off the post with Main beaten again, the visitors scrambling the ball clear.
In the 64th minute, though, Kyle helped himself to a second after Main ran from his box to almost the touchline to make a clearance that was partially blocked by Killie striker Conor Sammon.
When the ball broke back to Kyle 30 yards from goal, the former Coventry and Sunderland man quickly volleyed back towards the empty net and the chasing Saints keeper could not stop it bouncing in.
The visitors appeared shocked that they had fallen so far behind in a game which had hitherto posed little danger.
St Johnstone pushed forward in search of a lifeline, with all three substitutes on, but there was a sense of helplessness running through their ranks.
In the second added minute of four, Wright headed a Grainger corner into his own goal but it was too little, too late.