Mckay lobbed home after Kilmarnock were caught out by a ball over the top 10 minutes into the second half as Inverness restored their three-point lead over Celtic, who had earlier beaten Hearts.
Richie Foran had headed home from close range to give Thistle an early lead and they deserved the points despite Kilmarnock improving after a poor first half.
Although Killie started the second half strongly, only a freak ricochet off Barry Nicholson prevented Caley Thistle from securing a fifth clean sheet of the season.
Mckay restored the lead five minutes later and Inverness defended stoutly to seal the points in front of only 3,063 fans as Killie continue to seek their first win under Allan Johnston.
Johnston, who had unnamed injury concerns, was without Rory McKenzie and Darren Barr but on-loan Dundee United forward Michael Gardyne made his first start.
Left-back Rory McKeown also came in with Jeroen Tesselaar moving into the centre of an inexperienced back four.
And, while Caley Thistle started in determined fashion, their opening goal also came as a result of some statuesque Kilmarnock defending.
No home player reacted when McKay headed down James Vincent’s cross and Aaron Doran hooked the ball across the goalmouth for the unmarked Foran to nod in.
Gardyne and Doran fired over with decent efforts at either end but it was the visitors who were imposing themselves on the game.
The home fans vented their displeasure after McKeown’s over-hit passback from just inside his half went out for a corner and Inverness almost made them pay.
Gary Warren met Shinnie’s delivery with a powerful looping header which was heading for the top corner but Jacobs was well-placed to clear off the line.
Gardyne produced the first real threat for Dean Brill after the half-hour mark as he turned 25 yards out and fired a bouncing left-footed strike that the goalkeeper pushed wide.
But there was another warning in defence for Kilmarnock before the break when Mckay got away from Jackson Irvine to meet Doran’s cross but the delivery went just too far beyond him to allow a clean strike.
Johnston replaced Gros with Rabiu Ibrahim at half-time and his team should have been level when Kris Boyd and Gardyne linked up well in the box, but the loan forward blazed over from 12 yards.
Killie had a penalty claim rejected by Steven McLean when Jeroen Tesselaar’s strike appeared to come off David Raven’s arm, but they soon levelled on the break.
Rabiu collected the ball on the left wing and knocked it in front of the run of Nicholson. The back-pedaling Graeme Shinnie got there first to slide in but his clearance from just inside the box bounced off the shins of Nicholson and inside Brill’s near post.
The Highlanders had looked capable of stepping up a gear if necessary in the first half but their swift reply came out of the blue.
Killie were on the front foot when Josh Meekings launched a clearance from midway inside his half and Irvine was caught flat-footed. McKay ran clear and showed excellent composure to lob Samson with his left foot.
Manuel Pascali, who had only had a few minutes of action this season after a long-term injury, replaced James Fowler in midfield but his first significant contribution saw him booked for bringing down Nick Ross.
Boyd hit the outside of the post from a tight angle with 12 minutes left after holding up a long ball but Inverness otherwise proved too organised and committed for the home side to break down.