Humphrys’ quality shone through the gloom at a fogbound LNER Stadium, despite spurning a brace of first-half chances.
And when York centre-back Tyler Cordner misjudged a header on the hour mark, the 26-year-old charged clear and calmly rounded David Stockdale to bag his ninth goal of the campaign.
Wigan – wasteful throughout – then had to survive a late barrage from the National League side, who should have scored deep into stoppage time when Lenell JohnLewis miscued a free header just six yards from goal.
“The last three or four minutes got a little bit nervy but I’m really happy,” said Maloney, who famously won the FA Cup with Wigan as a player in 2013.
“I thought we played pretty well and it was a brilliant finish from Stephen. He’s got so much talent, so much speed one-v-one. He’s a player in form and hopefully he’s found a home here.
“Stephen came back from pre-season in great shape. He’s a lw ay s been a brilliant athlete but all the gym work and the training sessions – none of that matters.
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