Michael Rose's free-kick flew into the side netting for Colchester early on before County took a 17th-minute lead through Bishop, who volleyed in first time from Judge's free-kick despite Rose's attempts to keep it out on the goalline.
Jabo Ibehre headed straight at County goalkeeper Bartosz Bialkowski and Marcus Bean curled a shot just over for Colchester.
But Francois Zoko fired straight at U's goalkeeper Mark Cousins from close range and the Magpies doubled their advantage just before the break through Judge, who prodded in from just inside the area from Zoko's assist.
Bialkowski denied Ian Henderson early in the second half following a sweeping attacking move, but the Magpies were a threat on the break and Judge almost made it 3-0 when he fired over from 18 yards after a fine breakaway move.
Henderson's header clipped the crossbar for Colchester before the end, but it was County's night.