Slovakian Sagan edged out German Phil Bauhaus in a photo finish, with Dane Magnus Cort Nielsen third at the end of the flat 170km stage from Breda.
The week-long stage race, formerly know as the Benelux Tour and then Eneco Tour, is ridden through Belgium and the Netherlands.
Olympic champion Greg Van Avermaet is also in the field, along with German sprint ace Marcel Kittel.
Having crashed out of the Tour de France after winning five stages, Kittel was making his comeback to top level competition but could finish only 34th after being boxed in the sprint finish.
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