The Staggies extended their unbeaten run to 24 matches at New Douglas Park as early goals from Colin McMenamin and Scott Boyd put paid to Hamilton's chances inside 16 minutes.
Accies eased to a 5-1 win the last time Derek Adams' side made the trip to Lanarkshire but, as they have seen their title chances unravel, County have gone from strength to strength as they bid for a place in the Clydesdale Bank Scottish Premier League .
The 2-0 defeat leaves Hamilton 22 points off the pace in mid-table, but Stewart is determined not to let their season fizzle out as Reid's young squad look to finish with a flourish.
He said: "County are an experienced team and they took advantage of our individual mistakes, the first of which was mine, unfortunately. They are a good team and you can see why they are top of the league.
"They didn't have that many youngsters in their team on Saturday and even the guys on the bench know what it takes to play in this league.
"I thought we played quite well when we had the ball, but we weren't good enough without the ball.
"The results will come for us. We have a lot of young guys in the team at the moment, with a few experienced players in there as well.
"We still have plenty to play for this season and, of course, we have the Ramsdens Cup final coming up against Falkirk on Sunday, April 1."