Machel Baker and Brandon Strain-Goode were the ones who warranted the red cards.
NJIT outshot Quinnipiac 22-6 for the game while Bobcat goalkeeper Josh Lavallee had six saves in the loss, three in each half.
The Bobcats will head back to conference play Friday when they host St.Francis (Pa.) at 2 p.m. on the Quinnipiac Soccer Field.