Fabio, who has carved out an early role as the layoff assist king, scored a stunning first MLS goal in the 37th minute.
Duncan doubled the Red Bulls lead in the 56th minute with his first goal of the season.
Nashville have forged a reputation as a come-from-behind team early in the season, which made Carlos Coronel’s 61st-minute save at the edge of the six-yard box of a dangerous shot by Randall Leal even more vital for the hosts.