Waalwijk, who held champions Ajax to a 0-0 draw on Saturday, picked up just their second league win of the season, having gone two goals ahead within 15 minutes at the Mandemakers Stadion.
Belgian defender Kenny Van Hoevelen, who was later sent off, edged the home side in front after seven minutes when he headed home a free-kick from the left.
Erwin Koeman's men doubled their advantage soon after as midfielder Sander Duits converted fromn the spot after Robert Braber was fouled in the area.
And Breda's Sepp De Roover diverted a Romeo Castelen cross past his own goalkeeper 15 minutes from the break to hand Waalwijk a three-goal cushion at the interval.
It could have been four in the second half when a penalty was given for a foul on Castelen, only for Jelle Ten Rouwelaar to save Duits' spot-kick.
Despite Van Hoevelen being shown a second yellow card 14 minutes from time, Waalwijk were comfortable and held on to leapfrog NEC into 17th place, three points off safety.
Breda, who beat Go Ahead Eagles 5-0 last time out, would have moved into the UEFA Europa League play-off places with a win.
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