Hayes popped up with the winner in the 41st minute. The former Barnsley striker flicked the ball over the head of centre-half Adam Virgo before calmly firing past keeper Dean Gerken. It was his second league goal of the season since his summer move from Oakwell.
Colchester were not at their best and they are still waiting to record their first home win of the season, which is rather ironic when considered how well they performed at Layer Road in their first season in the Championship last term.
The U's had mustered just two points from a possible 12 at home, but they can count themselves unlucky not to have been given a penalty in the first half.
Winger Mark Yeates appeared to be bundled over in the box by Scunthorpe left-back Kelly Youga, but referee Mr Walmer declined to give the decision, as did his assistant, who was in an even better position to see the incident.
A penalty then may have changed the course of the game, but Hayes struck soon afterwards and Colchester never really looked like fashioning an equaliser in the second half.
In fact, Gerken remained the busier of the two keepers and he pulled off good saves to thwart Hayes and Jonathan Forte after the break.
Too often, Colchester's final ball let them down. Their crossing was poor and striker Kevin Lisbie was guilty of missing a couple of good opportunities with his head.
Fellow striker Clive Platt threatened deep into injury time, but his header from Yeates' corner flashed wide of the near post and that was the U's last chance.
Yeates had been the star of the show at Blackpool the previous weekend, thanks to two excellent free-kicks, and he curled a free-kick from a similar position narrowly wide against Scunthorpe. But it was not his or Colchester's day.