Ambrose held off a late challenge by Joey Logano, finishing three seconds ahead and notching his third straight victory in the event.
He joins Terry Labonte as the only drivers to win three consecutive Nationwide races at Watkins Glen.
Kevin Harvick ended in third place, followed by points leader Brad Keselowski and Kyle Busch, who fell short in his bid to collect a record-tying 10th Nationwide win this season.
Keselowski's fourth-place showing allowed him to widen his lead over Carl Edwards to 327 points. Edwards had engine problems Saturday and wound up finishing 33rd.
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