City, without several leading attacking players including Andy Cook, Alex Pattison and Tyler Smith, were poor in the first half and were unceremoniously booed off after a dire display against Paul Hurst’s Mariners.
A clinical header just before the interval from Danny Rose compounded supporters’ angst.
City, who switched to a back four from a 3-5-2 formation on the resumption, showed more intent and threat going forward in a 4-2-3-1 system.
But they had to wait for the 89th minute for their leveller, with their first effort on target.
Full debutant Bobby Pointon, whose endeavour caught the eye in the second period, set up interval substitute Alex Gilliead, who netted with a fine right-footed drive from just inside the box.
It was the midfielder’s first goal since netting in this same fixture on April 1, as the Mariners’ winless streak against City extended to 19 games.
Hughes said: "I think in the second half, we took the game to them. We had to make a few changes.
"Listen, it wasn't easy for us. We had four home debuts so there's a little bit of disruption to our playing 11.
"We had to move things around a little bit.
"In the first half, we had a plan to get a good press on and didn't do that in any way, shape or form and had to change it very, very quickly.
"In the second half, we went to four at the back and that helped us a great deal and then really forced the issue and got the goal we deserved.
"All in all, in the second half, it maybe - just maybe - makes up for the first half.
"The change of shape helped. We just needed to stop their backline just having comfortable possession and we needed to get on the front foot and effect them as an opposition as we didn't really do that in that first half.
"We changed the shape and had two wingers out of there and they were up against the two full-backs which was the out-ball for Grimsby in the first half.
"In the second-half, we stymied them."
On the performance of local lad Pointon, he continued: “I thought he was excellent today. The intention wasn’t really to give him 90 minutes.
“We thought we need to be fair to him. He’s only a young kid but he was a great creative outlet for us.
“He really took the fight to Grimsby in that second half once we got him on the ball.
"We know he’s got good qualities. He’s a conscientious kid who wants to do well and he worked exceptionally hard as they all did in that second half.
"It was just a case of understanding what we needed to do. We needed to get on the front foot.”