
The win brings New York (53-50) to within two games of the first-place Nationals (54-47) in the National League East.
Flores homered off Washington reliever Felipe Rivero (1-1, 2.11 ERA), who had put in two perfect innings of relief before the leadoff homer by Flores.
Nats starter Gio Gonzalez gave up a run on four hits in four and two-thirds hard innings, throwing 105 pitches, striking out six and walking four.
Mets ace Matt Harvey went seven and two-thirds innings, giving up a run on five hits, striking out nine without issuing a walk.