In cooler conditions compared to Friday afternoon's FP1 session, owing to the 7am start to proceedings in Brooklyn's Red Hook district, the drivers aimed to start running early to try to clear up some of the dust pervading the circuit.
Nyck de Vries was first to get within a second of the Friday times, setting a 1m10.693s, before countryman Robin Frijns punched in a 1m10.157s to get his Envision machinery to the top.
He was accosted by teammate Nick Cassidy, who displaced de Vries for second - before the Mercedes driver returned to the top with a 1m10.121s.
Andre Lotterer was then first to surpass the Friday times on a full 250kW power lap, posting a 1m09.353s - as Porsche teammate Pascal Wehrlein popped up into second with a lap 0.8s behind.
Frijns returned to headline the session for mere seconds, shading Lotterer by 0.03s, before de Vries displaced him with a 1m09.306s.
Jean-Eric Vergne then grabbed a 1m09.281s to pick up control of the session, before Stoffel Vandoorne went a tenth and a half faster - but both were surpassed by Lotterer with a 1m09.073s.
The times were then brought into the 1m08s by Wehrlein, but he was brushed aside by Mitch Evans, who held the best time of the session until the final few minutes - before da Costa displaced him with a 1m08.684s which ultimately proved to be the headliner of the session.
Evans' time was good enough for second overall, as Andretti's Jake Dennis claimed the third-fastest time in the American squad's home round.
Wehrlein ended the session in fourth ahead of Frijns, who led Envision's charge as Cassidy struggled with traffic on one of his fliers.
Vergne dropped to sixth, next to former teammate Andre Lotterer in the timing board, as Vandoorne and championship leader Edoardo Mortara were eighth and ninth quickest. Antonio Giovinazzi made his way into the top 10, 0.008s off of Mortara's best.
Vandoorne had headed FP1 with a late effort to depose Sergio Sette Camara from the top of the times.
The Dragon driver had beaten the more established frontrunners with a 1m10.135s, but Vandoorne fired in his best time before the chequered flag fell - clocking a 1m09.836s to hold the overnight bragging rights.
Formula E New York E-Prix I - Practice Results
FP2
FP1
