Terry Butcher's visitors created more clear-cut chances but could have been denied all three points had David Goodwillie converted a simple opportunity late on.
Thistle goalkeeper Dean Brill had to be alert in the opening stages to deal with a pair of shaky back-passes, while at the other end a James Vincent effort was deflected wide.
The breakthrough came in the 20th minute - Richie Foran's pacy cross breaking for McKay to coolly lift the ball beyond the reach of Radoslaw Cierzniak for his second of the season.
United responded only for John Rankin to fire a volley wastefully high and wide, and Gary Warren could have punished his folly had he directed his header on target before half-time.
In the 55th minute, Sean Dillon had to be alert to prevent Aaron Doran from doubling the advantage and a quarter of an hour later, Goodwillie passed up a gilt-edged chance to level.
Gary Mackay-Steven was the architect, breezing past his marker and producing an inviting cross to the far post, where Goodwillie somehow turned the ball away from goal rather than convert.
In the closing stages, a perfect cut-back from McKay gave Graeme Shinnie a clear sight of goal but although he dragged wide, Inverness held on to their slender lead and remain top of the pile.