Gilchrist, 19, scored the only goal of the game, having netted his first senior goal for the Clarets in their first pre-season game, an 8-0 victory over Austrian minnows Grossklein.
He came off the bench to strike in the 73rd minute as boss Sean Dyche gave some of his young squad players the chance to shine against James Beattie’s men.
Goalkeeper Matt Gilks had to make a superb early save to stop Josh Windass’ long-range bullet. On 23 Burnley had the ball in the net, Danny Ings pouncing on a rebound after Reds keeper Iain Turner had blocked Kieran Trippier – only to be denied by an offside flag.
Marvin Sordell’s volley whistled just past the post but the hosts clung on until half-time, when Dyche made wholesale changes.
Another new signing, Lukas Jutkiewicz, had another effort ruled out for offside, but Scott Arfield cleverly set up Gilchrist to score the winner.
After the match, Dyche told Sky Sports News: "It's really about fitness. I thought it was a good game for that reason. We had a really mixed group, a lot of young players.
"The one thing that we know is that there are gaps in our team. And we've got to fill them. There is a lot of work to be done with these young players to get them to first team level.
"They need to know where the gaps are, they need to know where they stand in the hierarchy of our club. It's a great chance, pre-season, for them to experience what it is, against our more senior, rounded players. They will have learned from that.
"It's early pre-season. We had a game over in Austria. The main first-team players have had a half each. In my mind there are players that we like, players who will start the season.
"But we want to add to the group, we are still in the market. There’s things beginning to build."
Dyche ruled out a move for Watford striker Troy Deeney, insisting the Clarets cannot afford him.
"I don't know what club we are! There must have been a financial bypass with linking us with someone for £8million," he said.
"He's amongst many players I admire, good players. But we've got a certain brief from the club that we have to work to. The club has a base to build from, financially. We can't entertain £8m players, I can assure you of that."
Whilst Dyche admits he is dealing in the lower levels of the transfer market, the challenge they are up against this season was highlighted on Friday.
Their opening opponents, Chelsea, re-signed Didier Drogba, but Dyche was unmoved.
"There's an obvious reality – we are going to be underdogs in every game we play," he said. “Probably the biggest underdogs there has ever been in the Premier League.
"But we all know the underdog's story – so let’s see how it develops."