RB Leipzig rescued a 2-2 draw against PSG with a stoppage-time penalty but the result saw them knocked out of the Champions League on Wednesday.
The Dutchman, who had struggled this season after joining from Liverpool, struck in the 21st minute and headed in another goal six minutes before halftime.
Substitute Dominik Szoboszlai did better from the spot in second-half stoppage time, however, to rescue a point for the Germans.
The Germans, looking for a win that would boost their slim chances of a knockout stage spot, had made a barnstorming start when Nkunku headed in at the near post eight minutes into the game.
The hosts could have doubled the advantage when they were awarded a penalty four minutes later but Silva's tame effort was stopped by keeper Gianluigi Donnarumma.
He struck again in the 39th, heading in his second goal of the evening and celebrating it only after a lengthy VAR review.
Mbappe went close to scoring on the stroke of halftime but keeper Peter Gulacsi pulled off a reflex save to deny the French striker, who also missed a golden opportunity early in the second half.
With the French backline far from solid, Leipzig constantly found the spaces to get into the box but they struggled with their finishing and Szoboszlai missed the target with their best chance.
The Hungarian, however, made amends when he stepped up to take a stoppage-time penalty, awarded for a foul on Nkunku, and equalised to earn his team's first point in the competition and keep them in the running for a spot in the Europa League.
"We created a lot of opportunities but also gave a few away and that's why they stayed in the game," Wijnaldum said. "At times we made it easy for them."
"If you look at the end of the game we lost the ball too often. We also did not convert our chances. Maybe Leipzig deserved the point.
"I work hard every day and I'm getting to know my team mates better. Let's hope I can continue this form," he added.