Stockport-born teenager Daly, 18, came off the bench to net a stoppage-time strike for Town, who dug deep to secure their first victory in six matches.
Alongside Daly, it was also an evening to savour for 20-year-old centre-back Edmonds Green, who was handed a Championship debut in an unaccustomed right-back role and played his part in the club securing a clean sheet.
Edmonds-Green, who has recently been recalled from a loan spell at National League side Bromley, said: “Everyone is buzzing after a last-minute winner. We have just got to take this moment into Saturday.
“It is good to see Academy boys score and it just shows that we are working hard. I have worked hard for this moment and am proud of myself.
“We were just waiting for that one chance and obviously it came to Matty and he took it well. He is probably shocked and cannot believe what has happened.”
On his league bow for the Terriers, he added: “Playing out of position, I was a bit nervous at first. But when I got into it, I thought I did really well.
“Schnids (Chris Schindler) helped me a lot and we had just got to make sure that we talked all of the time. I do not feel inexperienced. When you get going, you are just on the pitch playing and there’s leaders next to you such as Hoggy (Jonathan Hogg) and Schindler helping you.”
Town manager Danny Cowley revealed his side almost failed to make it to The Valley following traffic chaos in the capital.
The Terriers’ team bus got stuck in the Blackwall Tunnel following an earlier accident, with kick-off delayed until 8pm.
Cowley said: ““To finish the game with two young boys, and for Matt Daly to come out of our academy to find the winner, is probably why we all love football and is probably why nearly 900 Huddersfield Town supporters on a cold wet Tuesday night found their way to Charlton.
“It has definitely been a really tough period for us with the amount of injuries we have picked up and we started with 11 right-footers – only the second time I’ve done that in a 13-and-a-half-year managerial career.”