Bayern Munich's 3-1 win over Mainz earlier in the day had set the stall out for Leipzig, and Julian Nagelsmann's side looked to be heading to a second straight defeat when it went 2-0 down in the first half.
Alassane Plea scored a stunning goal for Gladbach in their defeat of Mainz last time out and was on target again to put the visitors ahead 24 minutes in, slotting home after fine work from Marcus Thuram and Oscar Wendt.
Gladbach doubled its lead 11 minutes later when Jonas Hoffman scored his first league goal of the season.
Leipzig rallied after the break, half-time substitute Patrik Schick making a quick impact with a low strike before Plea then saw red after receiving two yellow cards in the space of seven seconds, both for dissent.
Leipzig then made its numerical advantage count in the 89th minute, Nkunku thumping in a superb shot from the edge of the box to keep his team in second place, a point behind new leader Bayern.