New York, needing a victory to keep their season alive, took the lead on 22 minutes after Costa Rica international Alonso Martinez worked a clever one-two with Mitja Ilenic before sweeping a low finish past Cincinnati goalkeeper Roman Celentano.
Brazilian defender Thiago Martins doubled New York's lead five minutes before half-time, heading in at the back post after a free-kick from wide on the right sowed confusion in the Cincinnati defence.
Third seed Cincinnati hit back on 65 minutes with a superb individual goal from Argentine forward Luca Orellano, who nutmegged his marker before unleashing a thumping left foot shot into the top corner to make it 2-1.
Cincinnati pressed relentlessly for an equalizer in the closing stages, and Zimbabwe international Teenage Hadebe should have levelled in the 80th minute but blasted his close-range shot straight at New York goalkeeper Matt Freese.
New York made the game safe in the closing minutes of stoppage time as Uruguayan midfielder Santiago Rodriguez won a penalty, scoring it himself with a cheeky chipped 'panenka' down the middle of the goal.
Game three in the series will take place in Cincinnati on November 9th.