It extended the Magpies' club-record run of unbeaten away league matches to 18, stretching back to February.
Scunthorpe, looking for a third successive league win since the return of Brian Laws as manager, dominated much of the first half. They took the lead after 13 minutes when full-back Christian Ribeiro cut into the box from the right and steered a low, left-foot shot into the far corner of the net for his first goal for the club.
County were back on level terms in the 34th minute when a right-wing cross from Alan Judge found the head of Hughes. But the Iron came storming back with leading scorer Leon Clarke crashing a header against the crossbar before they regained the lead in first-half stoppage time when midfielder Damien Mozika popped up on the edge of the six-yard box to fire home a low cross from Riberio.
Hughes was unlucky not to equalise again after 55 minutes when he glanced a header from Alan Sheehan's free-kick against the outside of a post. The visitors thought they were level in the 63rd minute when a long-range shot from Sheehan found its way into the net, only to be ruled out for an offside infringement.
Five minutes later Scunthorpe were reduced to 10 men when skipper Paul Reid was sent off following an aerial challenge against substitute Yoann Arquin. County took advantage to finally equalise in the 82nd minute when Hughes forced the ball home from a corner.