Four of the six goals arrived in an entertaining second half, and former pacesetters Hamilton are now without a win in three matches.
However, it was the Accies who opened the scoring at the Caledonian Stadium where Tony Andreu’s 30-yard free-kick found the bottom left-hand corner of the net on 17.
At this stage Hamilton were on course to return to the summit themselves but their advantage lasted just eight minutes as McKay levelled matters with a low shot from inside the box, after latching on to a Marley Watkins cross.
The remainder of the opening 45 minutes yielded chances for both sides, and especially for the hosts.
James Vincent nodded wide, McKay went close, while Watkins had a header saved by Michael McGovern. At the other end Dean Brill saved from Darian MacKinnon but the teams turned around locked at 1-1.
The hosts started the second half the stronger and duly took the lead in the 59th minute when defender Gary Warren headed home Greg Tansey’s cross following a corner.
And Caley Thistle extended their advantage on 68 with McKay grabbing his second from close range after being set up by Watkins.
Yet Hamilton gave themselves some hope four minutes later as Andreu netted his second of the afternoon thanks to Mickael Antoine-Curier’s assist.
But any hope of Hamilton snatching a late equaliser for the second week in a row was snuffed out by Vincent who clinically converted a flick-on by the influential Watkins.
The win took Inverness from fourth to first in the table, although Celtic’s late victory at Aberdeen saw them go top of the table on goal diffference.