Justin Devenny also opened his international account, while in the first half a Jamie Reid strike was cancelled out by Aiman Dardari.
Charles struck less than 30 seconds into the second half and, after Luxembourg defender Seid Korac was shown a second yellow card, Devenny’s 69th-minute strike secured Northern Ireland’s first competitive away win since March 2023.
Sunday’s trip to Cologne could bring a Germany backlash after they crashed to a shock 2-0 defeat in Slovakia.
But Michael O’Neill’s side have made a perfect start in Group A and Southampton midfielder Charles will be targeting back-to-back wins.
“I can’t wait. We’ve got a lot of confidence. They’ll be coming out even stronger but I’m looking forward to it,” said the 21-year-old.
“It’s unbelievable. It was a good start but it was a tough first half. In the second half we dug in, scored early on and finished off strong.
“I nearly got one in the summer. I’m buzzing and it meant so much. It’s incredible.
“At half-time Michael wanted us to get more pressure on the ball and that showed straight away. They are a good team, but when we pressed higher we forced mistakes.”
Anthony Moris kept out Isaac Price’s penalty but Reid pounced on the rebound.
Jamie Reid
The hosts – under new management with Jeff Strasser 17 days into the job – equalised when Daniel Sinani’s neat flick released Dardari, who skipped beyond Paddy McNair as he cut in from the left to hit a low shot beyond Bailey Peacock-Farrell.
In first-half stoppage time Devenny’s free-kick clipped the top of the crossbar after a foul on Trai Hume.
After the restart, Conor Bradley’s low cross deflected out to Charles whose strike took a nick off the hapless Korac on its way in. Korac’s red card helped Northern Ireland see the job through.
Goalscorer Devenny said: “It’s the first win of campaign and we want to keep building. There’s a long way to go but we can’t start any better than that. It was a proud moment to get my first goal.
“The fans were out in their numbers and you could hear them from start to finish. Hearing that noise when scoring and seeing the smiles made me happy.
“Michael (O’Neill) said well done but we can be better than that. You can’t dwell on the win and you have to look ahead to the next one.
“It’s exciting times. Germany are a great side and you want to be challenged against top players. They might have a point to prove but we’ll stick to our game plan.”
O’Neill now fears a Germany backlash on Sunday after some stinging criticism from their media.
“It’s not the result we wanted,” said the former Stoke City boss.
“Going to Germany was going to be tough enough but now they are going to be heavily criticised in the media.
Justin Devenny
“As I said to the players, if we go home with three points it’s a good trip, if we go home with more it is a great trip, and we have the chance now to make it a great trip.
“I thought we started the game very well, we were on the front foot and the penalty helped us obviously.
“We dropped a gear after the goal, let them into it and the goal was coming. We had to get into them at half-time as there were things we could have done better but we got the reaction we wanted.
“The red card helped, but I think it was a decision that was merited. We are delighted to get the 3-1 win.
“We pressed better and we played forward better in the second half. We are not a team that is good with slow possession, we are better playing forward earlier.
“I think because we scored early we thought this is going to be easy for us, but it was far from it and we had to reiterate that at half-time.”
O’Neill was encouraged by the performance of Eagles ace Devenny, who could have bagged a brace.
“That has been a problem position for us,” he added.
“That is not his natural position but Justin has the attributes to play there. Athletically and technically he is very good.
“At times it is tricky for him defensively with his distances, but all round he is a really good footballer, not only with the goal but the balls he delivers.
“We haven’t had a left footer like that since Brunty (Chris Brunt), so it is nice we have found him.”