The Terriers' team bus got stuck in the Blackwall Tunnel on their way to The Valley following an earlier accident.
Kick-off was delayed until 8pm and a lacklustre encounter looked certain to be heading to a goalless stalemate until Cowley made what proved to be a game-changing substitution with 14 minutes left.
Youngster Matty Daly emerged from the bench to replace Steve Mounie and settled a largely-forgettable encounter deep into stoppage time with a sweeping finish from Florent Hadergjonaj's assist.
The result moves the Terriers four points above the drop zone and is their first win in six games, although it almost did not happen thanks to the unexpected traffic gridlock.
Cowley said: "It is probably why we all love football. It is probably why nearly 900 Huddersfield Town supporters on a cold wet Tuesday night find their way to Charlton.
"It has definitely been a really tough period for us with the amount of injuries we've picked up.
"To have the issue in the build up, we were in the Blackwall Tunnel, there was an accident and we pretty much got stuck there for over an hour - it pretty much summed up the period we've endured.
"So to get here at 7.15pm and to find a way to get on the right side of it obviously makes us really pleased.
"You are stuck in the Blackwall Tunnel and there is no turning round - then you do start to worry.
"With the injuries we've had we might have been pleased prior to the game if we couldn't have got here. We managed to get here in the end. It wasn't ideal."
Cowley added: "We said to the group before there are many excuses but we know football doesn't care about excuses.
"We said it didn't matter what anyone threw at us, and however difficult it gets, we are going to stick together and dig really, really deep.
"We started the game with 11 right-footers on the pitch. It is only the second time I've ever done that in a 13-and-a-half-year managerial career, the first one being last Saturday.
"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."